Phyrexia All Will Be One gave this cube a lot of new toys, especially in Blue.

Elvish Visionary replaced by Contagious Vorrac.

The Visionary is just a generic card that goes into lots of Cubes, the Vorrac fits in better with my themes and provides a similar function.

Prophet of the Peak replaced by The Filigree Sylex.

Prophet of the Peak wasn't really contributing much to this cube. Given that this cube is all about "wacky counters" The Filigree Sylex puts Oil Counters into the mix and just fulfils a more useful function.

Dissolve replaced by Reject Imperfection
This cube has a bit of a "scry matters theme" in Mono Blue which I'm thinking of just cutting. I swapped Dissolve for Reject Imperfection, as Reject Imperfection plays into my far more prominent Counters theme.

Bloom Hulk replaced by Adaptive Sporesinger
Adaptive Sporesinger is just a lower cost version of Gloom Hulk which also Provides more versatility. Cubes work better with lower curves.

Contentious Plan replaced by Experimental Augury
Contentious Plan is a pretty weak card, Experimental Augury offers a strictly better version of the effect with power more in line with what I'm looking for.

Scavenged Blade replaced by Barbed Batterfist
Scavenged Blade requires a creature in play to set up "modified", Barbed Batterfist can set up "modified" all by itself.

Risona, Asari Commander replaced by Bladehold War-Whip

While Indestructable Counters definitely qualify as "wacky counters" and it pains me slightly to remove a card with them, ultimately this feels like the right call. Risona doesn't really synergise with anything else Red/White is doing in this cube, whilst Blade-Hold War-Whip definitely doe, providing both a creature token with Double Strike to buff up and a discount on future equip costs.

Siani, Eye of the Storm replaced by Hurkyl, Master Wizard
Siani only really players into "flyers matter" and "scry matters" neither of which are very prominent subthemes in my cube. Hurkl, makes an interesting addition to Red/Blue "non-creatuers matter" strategies. I am concerned that this card is a bit hard to parse though.

Murder replaced by Drown in Ichor
Tamiyo's Epiphany replaced by Vivisurgeon's Insight
Charmed Sleep replaced by Mesmerizing Dose
Into the Roil replaced by Serum Snare

These are all instance of replacing generic spells, with spells that Proliferate. It's a shame because I find some of the Phyrexian art a little gory and grim, but the effects on the cards just work better for the cube.

Thinking of potentially adding a Scheming Aspirant in future.