I was correct in assuming that MH3 be so rich in inclusions to this cube that posting the changes for the previous sets was worthwhile to navigate this update more comfortably.
Lots of MDFCs made the cut and two-colored boosters mostly went down to three basics to accommodate the extra utility land. Boosters still lacking removal had priority when distributing MDFC removal.

The green and black flares are meant as try-outs to see if free spells are truly too powerful.

Comprehensive list of booster changes:
Kozilek: tablet of compleation - glaring fleshraker
Purphoros: flameshadow conjuring - Herigast, erupting nullkite
Alharu: hopeful initiate - metastatic evangel
Emiel: flicker wisp - phelia, exuberant
Raffine: big game hunter - deem Inferior
Tayam: leyline prowler - emperor of bones
Yidris: lizard blade - party thrasher
Brago: Linvala, the preserver - genku
Locust: remand - tamiyo, inquisitive student
Locust: Island - rush of inspiration
Locust: solemn simulacrum - emraluls messenger
Kaza: melek, izzet paragon - ral, monsoon mage
Kaza: silundi vision - sink in stupor
Rakdos: blight step pathway - blood soaked insigh
Hamza: Kurbis, harvest celebrant - guardian of the forgotten
Hamza: Arwen, mortal Queen - evolution witness
Tstyova: myriad landscape - bridgeworks battle
Radha: strider - territory culler
Teysa: Adeline, resplendent cathsr - muster the departed
Teysa: crowded crypt - Warren soultrader
Urza: buried ruin - archway of innovation
Wort: kodama's reach - flare of cultivation
Wort: mountain - pinnacle.monk
Wort: forest - stump stomp
Stickfingers: coffin queen - grist, voracious larva
Stickfingers: forest - revitalizing repast
Selvala: wirewood lodge - disciple of freyalise
Lurrus: null priest of oblivion - accursed marauder
Lurrus: Swamp - spy masters vault
Scarab: temple of deceit - sunken palace
Nymris: swamp - waterlogged teachings
Kels: access tunnel - fell the profane
Atraxa: deepglow skate - dreamtide whale
Chandra: mountain - myriad landscape
Falco: bioessence Hydra - deepglow skate
Jetmir: horizon canopy - strength of the harvest
Emiel: plains - horizon canopy
Emiel: kogla, Titan ape - somberwald stag
Korvold: xira, the golden sting - skittering precursor
Volrath: Kodama of the West tree - basking broodscale
Saffi: felidar guardian - eladamri korvecdal
Golos: mairsil, the pretender - ertha jo, frontier mentor
Isshin: krenko, tin Street kingpin - anim pakal, thousandth moon
Isshin: bolt hound - firemane avenger
Teshar: emerias call - monumental henge
Abdel: Castle ardenvale - emerias call
Kess: jeleva, neihalias scourge - ashling , flame dancer
Djeru: plains - razor grass ambush
Derevi: recruitment officer - wind dancer
Anhelo: terminate - flare of malice
Zacama: evolving wilds - horizon of progress
Windgrace: riveteers outlook - evolving wilds

Two new cycles of dual-lands mix up the man's base for a lot of boosters. Temples mostly leave the cube entirely.
Two boosters were changed entirely (see prior updates).

Here is the complete list of changes to every booster:
Alesha: selfless spirit - delney, streetwise mentor
Alesha: alloy myr - oasis gardener
Abdel: Invasion of Belenon - resolute reinforcement
Abdel: legions landing - prismatic lens
Abdel: Lulu, loyal hollipgant - Case of the gateway dxpress
Anhelo: spellbinding soprano - deliberate?
Anhelo: deekah, fractal - Judith, Carnage connoisseur
Anhelo: Saruman - baral and kari zev
Atla: endraze forerunners - flamewright
Atla: mondrak, glory dominus - sandstorm slavager
Atla: mossfire valley - fabled passage
Alela: temple of silence - shadowy backstreet
Alharu: ajani - animation module
Animar: temple of mystery - hedge maze
Atraxa: port town - marsh flats
Brago: meneldor - wall of omens
Breya: scrapheap scrounger - esoteric duplicator
Breya: academy ruins - public thoroughfare
Breya: island - plains
Breya: marsh flats - bloodstained mire
Chulane: yasharn, implacable earth - white mane lion
Chainer: mountain - racuous theater
Derevi: canopy vista - overflowing basin
Dihada: temple of malice - delosate mire
Djeru: arena rector - onnake oathkeeper
Emiel: wall of omens - wall of blossoms
Garth: Ash barrens - Viridescent bog
Golos: jegantha - izzet locket
Goreclaw: defiler of vigor - moss diamond
Hofri: nahiri - brion stoutarm
Isshin: captain lannery storm - breeches, eager pillager
Isshin:Aurelia, the war leader - caesar, legions emperor
Jetmir: Chatterfang, squirrel general - selvala, eager trailblazer
Jetmir: Black market tycoon - we ride at dawn
Jhoira: mountain - ferrous lake
Jodah: contaminated aquifer - undercity sewers
Jodah: you cannot pass - Annie joins up
Karador: vengeful pharaoh - hollow marauder
Karador: priest of fell rites - honest rutstein
Kasla: restless bivouac - restless spire
Kess: dragons rage channeler - Eris, roar of the storm
Kess: bloodstained mire - Clearwater pathway
Kels+Gix: smothering abomination - tinybones, the pickpocket
Kethis: yawgmoths vile offering - vraska joins up
Kinnan: forest - restless vinestalk
Falco: irrigated farmland - sunglass prairie
Kolvori: the world tree - hidden nursery
Kozilek: waste - fomori vault
Kozilek: walking ballista - skittering cicada
Locust: temple of epiphany - thundering falls
Locust: Jace, vryns prodigy - duelist of the mind
Locust: fireminds vessel - bandits haul
Meren: temple of malady - underground mortuary
Nymris: zareth San - lobelia Sackville baggins
Omnath: ramunap excavator - bristly bill, spine sower
Omnath: aesi, gyre of the straits - Bonny pall, clearcutter
Prince urza: temple of enlightenment - meticulous archive
Prince urza: island - scene of the crime
Prince urza: bladegryff prototype - oltec matterweaver
Prosper: hoarding brood Lord - nobles purse
Prosper: tectonic giant - Magda, the hoardmaster
Raffine: dromors cavern - restless reef
Raffine: Clearwater pathway - dimir aqueduct
Raggadragga: forest - restless ridgeline
Saffi: plains - restless prairie
Scarab God: island - temple of deceit
Sedris: temple of deceit - contaminated aquifer
Sedris: noxious gearhulk - nulldrifter
Selvala: woodland bellower - leaf gilder
Sydri: dimir aqueduct - port town
Tayam: Agatha's soul cauldron - insidious roots
Tayam: temple of plenty - lush portico
Teysa: ravos, soul tender - Baron Bertram graywater
Teferi: thassa's intervention - three steps ahead
Teferi: lithoform engine - canyon crab
Tatyova: world shaper - on the trail
Teshar: sanwell, avenger ace - restoration specialist
Teshar: of herbs and stewed rabbit - salvager of ruin
Teshar: inspiring statuary - manakin (just add)
Toshiro: morbid opportunist - kaervek, the punisher
Wind grace: the mending of dominaría - world shaper
Wort: temple of abandon - commercial district
Yidris: mountain - mossfire valley
Ziatora: game trail - analyze the pollen

Isperia wasn't interesting to play and only had synergy surrounding itself as commander. I strive to have at least a few partner commander per booster to encourage creativity when designing the command zone.

Queen Kayla's theme of discarding small creatures and artifacts was too parasitic and narrow and fell flat even when paired with other "weenie" boosters. Pia Nalaar is more generally value-oriented while also caring about artifacts and tokens.

Lots of upgrades to the landbase, especially mono-colored. Cyclers from LTR and caves from LCI. Some restless manlands and the green cave haven't found a home yet but I have them filed to be included in a future update.
I will reduce the amount of updates to two per year going forward as implementing them IRL takes me too much time.

Comprehensive list of all booster changes:
Alesha: subira, tulzidi caravaneer - witchstalker frenzy
Kayla: battlemages brazers - inti, seneschal of the sun
Kolvori: moss diamond - the irencrag
Teferi: draining whelk - Horned loch-whale
Tayam: promise of bunrei - Agatha's soul cauldron
Kethis: isareth - Thalía and the gitrog monster
Korvold: tuktuk, the explorer - souls of the lost
Lurrus: vengeful strangler - cruel celebrant
Maelstrom: Sakashima - up the beanstalk
Animar: soul of the harvest - troyano, gutsy explorer
Atraxa: Elspeth conquers death - thrummingbird
Atraxa: forge of heroes - shattered sanctum
Chulane: greenwarden of murasa - woodland acolyte
Garth: coalition relic - alaundo, the seer
Goreclaw: bramble sovereign - the skullspore nexus
Grimgrin: ayara, widow of the realm - wilhelt, the rotcleaver
Saffi: adarkar Valkyrie - extraction specialist
Raggadragga: undermountain adventurer - viridian joiner
Purphoros: Hellkiste tyrant - trumpeting carnosaur
Purphoros: mountain - red cave
Prince Urza: foundry inspector - oaken siren
Omnath: khalni gem - rumbling rocklide
Omnath: harrow - entish restoration
Windgrace: entish restoration - harrow
Muldrotha: lord of the forsaken - akawalli, the seething tower
Meren: swamp - restless cottage
Sedes: fireflyx squad - Coalition relic
Kenrith: tazri, stalwart survivor - agatha of the vile cauldron
Toshiro: swamp - black cave
Isperia: plains - restless Anchorage
Hofri: plains - restless bivouac
Stickfingers: Kagha shadow archdruid - the mycotyrant
Stickfingers: demons disciple - Chupacabra echo
Urza: island - blue cave
Teshar: plains - white cave
Rakdos: swamp - restless vents
Anhelo: rocky tar pit - Frostboil snarl
Djeru: spinning wheel - gatewatch beacon
Chandra: Chandra heart of fire - Chandra, legacy of fire
Dihada: shattered sanctum - the grey havens
Kels+gix: swamp - the black gate
Drana: swamp - Troll of khazad-dum
Feldon: castle embereth - oliphaunt
Feldon: mountain - mines of moria
Kess: frostboil snarl - lorien revealed
Selvala: forest - generous ent
Zacama: stone-seeder hierophant - nature's lore
Tatyova: tatyova steward of tides - vinelasher kudzu
Tatyova: perennial behemoth - undergrowth champion
Tatyova: island - brave the wilds

I still had some 40.odd cards from the lotr expansions I wanted to include but couldn't quite find the right fit.
I also have two three boosters to still add after this.
Still gotta update the overview sometime in the future.
Comprehensive list.of booster changes:
Brago: restoration angel - meneldor, swift savior
Dihada: odric, lunarxh marshal - eomer, marshal of Rohan
Dihada: ob nixilis reignited - eowyn, fearless knight
Jhoira: jhoiras familiar - gloin, dwarf emissary
Jodah: cabaretti courtyard - great hall of the citadell
Jodah: the reaver cleaver - delighted halfling
Jodah: heros demise - friendly rivalry
Jodah: minsc and boo - nashi, moons legacy
Kaza: comet storm - flame of anor
Kethis: somberwald sage - inherited envelope
Kethis: the wandering emperor - Gideon, ally of zendikar
Garth: clever conjurer - ioreth of the healing house
Kolvori: Yisan the wanderer bard - Legolas greenleaf
Kolvori: Helm of the host - animists might
Korvold: glittering stash - the balrog, durins bane
Lurrus: mire triton - dusk // dawn
Lurrus: mishras bauble - Kayla's reconstruction
Lurrus: soldevi adnate - lotho corrupt shirrif
Eligeth: isolated watchtower - rivendell
Radha: tempered in solitude - nissa, resurgent animist
Radha: sunbirds invocation - strider, Ranger of the north
Anhelo: Cryptic pursuit - Saruman the white hand
Hamza: clay champion - Arwen, mortal queen
Hamza: basri's lieutenant - Slurrk, slime
Derevi: toski, bearer of secrets - edric, spy master of trest
Kels gix: burakos, party leader - Gollum, scheming guide
Kels: stronghold Assassin - death rattle oni
Kenrith: biomancers familiar - tazri, stalwart survivor
Alela: borrowed time - Conclave tribunal
Kykar: akoum, the soar8ng Wind - narset, eniightened exile
Meren: gonti, lord of luxury - smeagol, helpful guide
Nymris: Wavebreak hippocamp - faerie mastermind
Raggadragga: cryptolith rites - elven chorus
Sedris: worn powerstone - the balrog of moria
Atla: burn down the house - nesting dovehawk
Atraxa: kiora, master of the depths - master biomancer
Drama: burning rune demon - tymaret calls the dead
Hofri: terror of the peaks - nahiri, the unforgiving
Isperia: ojutsi monument - Malcolm, keen-eyed Navigator
Teysa: hero of Bladehold - Adeline, cathar
Urza: memnarch - karn, legacy reforged
Saffi: apex altisaur -
Tatyova: brinelin - Gretchen titchwillow
Vannifar: spark double - kiora master of the depths
Teshar: anointed peacekeeper - of herbs and stewed rabbits
Teshar: tocasias welcome - welcoming Vampire
Windgrace: springbloom druid - entish restoration
Atla: get rid of a green dual - many partings
Osgir: needleverge pathway - rustvale bridge

Adeline was a bit too narrow a booster to inspire a deck. Alharu, although it seems similar, has a lot more overlapping synergies.

I still want to test more Battles but for now this has to do.
List of all booster changes:
Dihada: acererak - djeru and hazoret
Omnath: Thalia's Lancer - omnath, locus of all
Abdel: call for unity - invasion of belenos
Queen Kayla: diviners wand - knight errant of eos
Kenrith: jodah, the unifier - omen hawker
Locust god: leadership vacuum - artistic refusal
Kykar: fateful absence - Invasion of segovia
Jhoira: phyrexian metamorph - yotia declares war
Elsha: prismatic ending - the brothers war?
Kinnan: génesis storm - Inga and esika
Selvala: hyrax tower scout - ancient imperiosaur
Alela: cruelty of gix - the eldest reborn
Atla: blasting station - Mondrak, glory dominus
Breya: treasure nabber - myr battlesphere
Carth: forest - swamp
Radha: vizier of the menagerie - augur of autumn
Chulane: augur of autumn - enlisted wurm
Derevi: sword of the animist - squall drifter
Drana: cemetery tampering - patron of the vein
Grimgrin: skyclave relic - culling the weak
Grimgrin: overcharged amalgam - ayara, widow of the realm
Nymris: kaito, dancing shadow - overcharged amalgam
Hamza: forest - plains
Hamza: marwyn, the nurturer - Kami of whispered winds
Hofri: opportunistic dragon - neyali, suns vanguard
Hofri: network terminal - skirk prospector
Isperia: duelists heritage - jubilant skybonder
Isshin: hellkite welp - bolt hound
Isshin: cheering fanatic - bitterthorn, nissa animus
Jetmir: Talisman of impulse - black market tycoon
Jetmir: Rhys, the redeemed - cadira, caller of the small
Kolvori: Esika, god of the tree - omnath, locus of mana
Kess: pongify - dragon's rage channeler?
Maelstrom: hajar, loyal bodyguard - averna, the chaos bloom
Osgir: slobad, iron goblin - dutiful replicator
Prosper: Talisman of Indulgence - hoarding broodlord
Prosper: hidetsugu - hedron detonator
Purphoros: hoarding dragón - Talisman of impulse (jetmir)
Raffine: ghastly discovery - lingering souls
Rakdos: brash taunter - Talisman of Indulgence
Raggadragga: lay of the land - cinder glade (Riku)
Riku: cinder glade - lay of the land (Ragga)
Scarab: Kairi, the swirling sky - raffine's silencer
Sedris: fallen Shinobi - kethek, crucible goliath
Sedris: phyrexian delver - seasoned pyromancer
Sydri: aerial surveyor - flywheel racer
Tatyova: scourge of fleets - new jolrael
Tayam: Kathril, aspect warper - archangel Elspeth
Urza: command beacon - seat of the synod
Windgrace: the gitrog monster - Invasion of lorwyn
Windgrace: Dakmor salvage - gemstone mine
Zacama: Farseek - invasion of zendikar
Atraxa: mana confluence - port town
Atraxa: path of ancestry - still figuring out

I find with these large lists that once I make a big update it becomes much easier to keep working on the list once everything is up to date. I usually end up making two or more updates.
Comprehensive list of all updates:
Greven chainer: +ghitu encampment
Prosper: +immerstrum skullcairn
Hofri: +needle spires
Raffine: Port town - dromars cavern
Scarab: +Port of karfell
Animar: +lumbering falls
Meren: +Swamp
Djeru: eldest reborn - Sorín, grim nemesis
Stickfingers: leyline prowler - werebear
Tayam: avacyns pilgrim - leyline prowler
Teferi: Sundering titan - thassa's intervention
Jetmir: Talisman of unity - undercellar myconid
Kayla: irencrag pyromancer - dismissive pyromancer
Kayla: mountain - skyclave cleric
Falco: grateful apparition - kasmina, enigmátic mentor
Feldon: birthing pod - Bogardan hellkite
Wort: cultivate - kodama's reach
Raggadragga: undercellar myconid - cradle clearcutter
Raggadragga: green suns zenith - lifeblood hydra
Raggadragga: chord of calling - genesis hydra
Raggadragga: Fanning the flames - apocalypse hydra
Riku: bonders ornament - rampant growth
Zacama: miraris wake - stone-seeder hierophant
Scarab: infernal idol - myr convert
Kozilek: leveled lotus - tablet of compleation
Sedris: undead butler - spitebellows
Drana: oriq loremage - undead butler
Garth: scion of draco - clever conjurer
Elsha: darksteel mutation - touch the spirit realm
Golos: bronze walrus - chamber sentry
Golos: replicating ring - bonder's ornamen
Eligeth: sigiled starfish - bronze walrus

I developed proliferate as a deck-theme in preparation for ONE and am very happy with how it fits with a lot of boosters. Planeswalkers or +1/+1 counters are all great synergies for a proliferate booster.
Dialing back the last bit of tutors that were still present in the cube.
Comprehensive list of booster changes:
Urza: Fabricate - eye of vecna
Scarab: sidisi - champion of wits
Grim-Grin: diabolic tutor - cryptbreaker
Brago: skyclave apparition - reflector mage
Brago: recruiter of the guard - whirler rogue
Kess: demonic tutor - maestros charm
Kess: spellseeker - see the truth
Kess: commune with lava - jeleva, nephalia's scourge
Anhelo: jeleva, nephalia's scourge - kolaghan's command
Anhelo: squee, the immortal - expressive iteration
Alesha: imperial recruiter - plundering barbarian
Elsha: enlightened tutor - Levitating statue
Elsha: mirrormade - reckoner bankbuster
Kykar: expressive iteration - third path iconoclast
Kykar: krark the thumbless - akim the soaring wind
Atla: scute swarm - halsin, emerald archdruid
Sydri: rebbec, Architect of ascension - Mighty servant of leuk-o
Sydri: tale's end - surgehacker mech
Sydri: etherium sculptor - Aerial surveyor
Chandra: karplusan hound - contagion clasp
Chandra: oath of Chandra - volt charge
Chandra: renegade patrol - Jeskai, thrice reborn
Rakdos: Chandra, torch of defiance - sin prodder
Isperia: alrund, god of the cosmos - Inniaz, the gale force
Maelstrom: gilded lotus - lukka, boy d to ruin
Falco: gyre engineer - rishkar, peema renegade
Osgir: queen Kayla bin-kroog - slobad, iron goblin
Osgir: darksteel juggernaut - bronze guardian
Sedris: Egon, god of death - Bazaar trade mage
Sedris: lotus bloom - illuminator szeras
Nymris: overcharged amalgam - kaito, dancing shadow
Yidris: irenicus vile duplication - abaddon, the despoiler
Kethis: captain sissy - Drizzt o durden
Golos?: Mishra, eminent one - Mairsil
Korvold: body launderer - mahadi, emporium master
Jhoira: crystal shard - Saheeli, the gifted
Locust: grinning ignus - firemind vessel
Carth: vorinclex, monstrous raider - vraska, betrayal's sting
Riku: errant, street artist - irenicus vile duplication
Windgrace: uurg, spawn of turg - Conduit of worlds
Yarok: rishkar, peema renegade - farhaven elf
Garth: roon of the hidden realm - Tyvar, jubilant brawler
Jhoira: pia and Kiran nalaar - Chiss-goria, the forge tyrant
Feldon: seasoned pyromancer - Vulshok furnace
Toshiro: isochron sceptre - synthesis pod
Tayam: thrashing brontodon - cankerbloom
Fálco: brokers confluence - Ichormoon gauntlet
Falco: kodamas reach - armored scrapgorger
Prince Urza: kappa cannoneer - unctus, grand metatect
Volrath: necroskitter - serrated arrows
Volrath: evil twin - tainted observer
Volrath: dreadship reef - thristing roots