Bitter Chill < Weakstone's Subjugation: While Subjugation is cheaper in the best case, that frequently requires taking a hit you'd rather not want to, and Bitter Chill replaces itself in the typical feel-bad case for these types of cards, which is a huge gain.
Cheeky House-Mouse < Dauntless Bodyguard: Bodyguard is a just a vanilla 2/1 on the turn you'd be happiest to play it. House-Mouse is another enabler for WR heroic that any white aggressive deck will want at a similar rate to Bodyguard.
Embereth Veteran < Frenzied Goblin: A Jackal Pup with upside is great, and missing in red at Peasant. Frenzied Goblin does do work in the right deck, but taxing a mana and being only a 1/1 on its own is rough.
Gadwick's First Duel < Founding of the Third Path: Founding frequently feels too awkward to use profitably enough to justify including in a deck. Duel is soft removal with plenty of value tacked on the end of it, plenty enough to at least try out.
Hearth Elemental < Reckless Impulse: I mostly see Hearth Elemental as Stoke Genius plus a (situationally) cheap beater as a bonus. Reckless Impulse is a totally playable card, but I'm happy to upgrade it with a card that has more gameplay on it.
Lord Skitter's Butcher < Phyrexian Rager: It's hard to find a cut in black 3mv creatures, I would put them at one of the strongest slots in the cube, but this little guy does it by my estimation. Rager's time has sadly come, and similar to Reckless Impulse I'm replacing it with a card that has more gameplay to be had.
Shrouded Shepherd < Aron, Benalia's Ruin: Aron hasn't played out as well as I hoped. It wants to go in an aggressive deck, but the mana cost means he can't always come down turn 3 and the ability tapping Aron means he can't even use his solid statline. It plays very slow in a deck that doesn't want it, whereas Shepherd will both clear the way and slam in hard.
Witchstalker Frenzy < Magma Jet: Magma Jet has always felt a little bad to use. Even with the scry smoothing out your future turns, 2 damage for 2 mana just isn't the rate you'd like it to be at. Witchstalker Frenzy is a very interesting kill spell that plays well in both aggressive and controlling decks, but isn't going to be immediately grabbed by spells matter decks.
Aether Gale < Dismiss: Dismiss ends up being too slow too often to keep its spot. I like the game reset that Aether Gale supplies over a clunky counterspell.
Pianna, Nomad Captain < Archetype of Courage: Archetype is fantastic on paper, but I've found aggro decks would much rather have more power/toughness than first strike. Decks that run archetype aren't running huge creatures that can avoid multiblocks with first strike, so the anthem is going to be generally better.
Anafenza, Kin-Tree Spirit < Knight of the Holy Nimbus: Swapping out a generically good creature with WW cost for a better one. Anafenza is a nonbo with GW tokens decks which does hurt it, but she's strong enough that it's okay anyway.
Kirtar's Wrath < Syr Alin, the Lion's Claw: Syr alin has always been a mediocre top end in decks that can be very choosy about any big spell, so it's on the chopping block for the first white sweeper available in peasant. This can enable more consistent WU and WB control decks, since there is a selection of sweepers in the cube now.
Gonti, Lord of Luxury < Crypt Rats: Gonti is an absolute house, and is exactly what black value decks are looking for. Crypt Rats is a valuable tool as a clunky harmful sweeper in the old peasant world where sweepers of more than -2/-2 were almost nonexistent. Now that a few have been added, it doesn't need to fill in for better spells.
Isareth the Awakener < Pawn of Ulamog: Pawn is a solid sacrifice payoff, but since it doesn't lead to direct damage or power on the battlefield it's on the low end of what those decks are looking for. GB decks have been lacking payoffs for filling the graveyard, and Isareth is a much more valuable card in those decks than what Pawn brings to sacrifice decks.
Gorex, the Tombshell < Bone Picker: Speaking of graveyard payoffs, wow! Bone Picker has always been theoretically excellent, but rarely lived up to its promise.
Yahenni, Undying Partisan < Gurgling Anointer: Anointer is a good and fun card, but black creatures have powered up so much with CMM that it can't keep up. Yahenni is just a better growing threat, and much harder to remove.
Skyline Despot < Magmaw: Magmaw is just too expensive of a sacrifice outlet compared to what the cube has at this point, and despot is insane.
Rorix Bladewing < Frenzied Saddlebrute: Adding 1 to the cost and having a more intensive color restriction is a trade I'm happy to make to get +1/+1 and flying. Losing the team haste enabler is noticeable, but it reads better than it plays. An opponent that can't kill Saddlebrute is dying whether or not future threats also get haste.
Rishkar, Peema Renegade < Yavimaya Elder: Elder is plenty of value, but it's so slow, and against anything but control you just can't afford to not affect the board to put lands in your hand. Rishkar provides both ramp and stats, the best of both worlds.
Goreclaw, Terror of Qal Sisma < Halana, Kessig Ranger: Halana has crazy theoritical value, but playing creatures out with 2 mana to spare is not what green decks are interested in. Goreclaw instead accelerates green's gameplan, rendering blockers irrelevant rather than fighting them.
Oviya Pashiri, Sage Lifecrafter < Cloakwood Swarmkeeper: Oviya's activated abilities are quite expensive, but having a consistent token source in the late game is nothing to sneeze at. This might be too slow, as swarmkeeper can beat down hard with a good runout, but this is a great midrange piece.
Rampaging Brontodon < Penumbra Wurm: It might die to doomblade, but boy howdy you're gonna die if you don't have removal.
Surrak, the Hunt Caller < Briarhorn: This essentially reads "5/4 haste for 4, your creatures have haste" which is scary in a green deck. Briarhorn is a nice combat trick, but it's not Surrak.
Judith, the Scourge Diva < Blightning: I love Blightning, but it's simply good, not synergistic. Judith is both good and synergistic, so she's going in.
Rhythm is better against control in some situations, but Grumgully is the better card most of the time.
Finks and Redcap used to both be in the gold section for their colors, and were eventually cut for more archetype support. However, the hybrid costs are easier to cast than a monocolored card would be, not harder. I picked the most likely color for both and made swaps there.