Keep in mind that adding new cards to the cube means also taking cards out, and the justification of other cards in the cube will also be affected. Also recognize that there is no one perfect version of the cube and revisions made are ultimately my decision.
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I've come up with a set of guidelines that I've used to put the cube together and make revisions. They are of course merely guidelines, though I at least ask that suggestions follow "replace X with Y because Z" and try to preserve the card ratios.
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1. The cube has 90 main deck monsters (20% or 18 are normal), 45 spells, 45 traps, 20 fusion monsters, 20 synchro monsters, and 20 xyz monsters. The numbers of monsters of different levels/ranks follow a curve. When swapping out cards, try to swap out cards with those of the same card type and level.
2. For cards that only interact with a particular type, attribute, archetype, or mechanic, the more representation the better.
3. 'Adapters', or cards that enable play of other cards, are healthy for the cube in moderation; this can include fusion substitutes, cards that change type/attribute/level, or generic search effects.
4. Cards that require specific other cards to work (like fusion spells) should have multiple usable combinations, unless a 2-card pair is worth the trouble of assembling or offers something unique.
5. Favor cards that disrupt players over ones that restrict them; the former is interactive and the latter is not. Restricting cards that do exist should at least require setup or offer plenty of chance to be played around.
6. Even in the cube cards aren't made equal, though their overall power levels should still be considered, and with context. For instance, the cube has plentiful ATK/DEF modifiers and attack stoppers while hard removal is kept more rare and costly, and self-summoning effects in the main deck are prevalent but are generally meant as means to an end.

Polymerization is too integral to Classic Fusions to hope you can pull it in your draft. Much like how MTG lets you have as many lands as you need to make what you draft work, I think you should let each player have 3 Polymerization so that they can make use of whatever fusion monsters they might have to pull. (I would then replace its spot in the Cube with Fusion Sage, or the other Fusion substitute cards like "Goddess with a Third Eye", "Mystical Sheep #2", Etc.)

Free Polys is an interesting idea. I'll play around with it and see how it affects pick choices. There's also plenty that can be done to add more subs or options past the current 10 fusion spells and King of the Swamp so I can always tinker with that.

The thing is, from playing with the real-life version of the cube I've found 'typical' fusion comes out to be a hoard-or-ignore thing where the spells aren't compelling choices anyway without already having materials, subs, and/or search; I've found they tend to naturally end up funneling to the few that would want to put them in their deck anyway (aside from the more splashable ones like Instant Fusion, Future Fusion, Super Poly, or Claw of Hermos).

Some fusions do inevitably end up being sided out for being unusable, though the same goes for synchros like the Synchron Warriors or xyz like Photon Strike Bounzer.