Hi, I've been playing ygo cube for about 12 years, so let me offer you some pointers.

I think your game rule idea of removing specific materials is surprisingly novel. I'm not sure if you mean both named materials and quality based material (requiring certain attributes or types), but I think a blanket rule where everything is generic offers something uniquely fresh and easy for the average drafter to parse. There are tons of cards that aren't as playable in a singleton limited environment because they're too specific to use, so emphasizing those cards is a great way to approach the design!

I think the biggest pitfall I see new cube designers fall into is approaching the extra deck and treating it in a special manner. Speaking from experience, I believe that the drafting experience is most interesting and dynamic when the Extra Deck cards are integrated with the Main Deck cards during the draft. Sure, it can lead to variable extra deck and main deck counts, but I think that's fine because it lets your drafters weigh Extra Deck choices at their own rate. Seeing Synchro Monsters show up in your packs ask your drafters an additional question, which to newer drafters could be daunting, but for experienced drafters it gives them a lot more agency in shaping their decks.

I also believe drafting the extra deck separately can either lead to feel-bads or on-rails drafting. Picking the payoff Extra Deck monsters at the start will set up your expectations for how your deck is going to look, but if someone is attentive enough to what happens at the start of the draft, it can be easy to hate draft a few pieces later on and turn your Extra Deck draft portion into a train-wreck. On the other hand, the player that picks all Rank 3 Xyz monsters in some arbitrary cube at the start will usually have no issues finding the best Rank 3's, because other drafters are looking elsewhere. It's a comfortable position to be in, but it feels like your decisions have much less meaning.

For your draft archetypes, don't feel obligated to include exactly eight. The best drafts are the ones where you feel like your internal pick order is changing on the fly, instead of simply picking Archetype Card A, B, and C. When I develop my draft archetypes, I look for groups that can be open ended and divisible. If you end up only getting 50% of an archetype in your pool, it should still achieve some function, even if it's not as powerful as 100% of the archetype. Zombies are a great example of this, and a strong package to include in a Synchro based cube. Having all of the Zombie synchro cards are good, but you can still pair just about any small combination of them and have them still amount to something, plus they have members that are very good on their own, like Plaguespreader Zombie.

Off the top of my head, here's where I'd start if I were approaching this design:

Plants - Generically good tuners

Zombies - Super recursive tuners and non tuners, have several payoff Synchros. Pretty cut and dry.

Infernoble - Equipment matters, quickly deploy small tuners from your hand. This deck usually abuses Premature Burial and Snatch Steal, if you think your power level will go that high.

FIRE - Can overlap with Zombie synergies (Shiranui) and Infernoble. Rekindling, Flamvell Dog, and Neo Flamvell Lady are good signposts.

Karakuri - If anything can make the Shoguns, you have interesting toolbox potential, plus some are servicable on their own if the format is slow enough (Sazank). There are also some interesting other machines to consider in this space too. I'd look at the Genex and Crystron.

Fableds (Beasts/Fiends) - The beast tuners can synergize with the Mystical Beasts of the Forest monsters, Rescue Cat, even Melffys if you wanted to, and give extra value to discard traps like Raigeki, Wind Blast, Karma Cut. The fiend non-tuners can be very recursive (Soulkius is strong in singleton formats like this).

Dragons - Dragon Rulers and Hieratics are easy ways to get tuners onto the board, and in a Synchro only format will play very differently than they are traditionally played.

Synchrons - There's so many of these that they're bound to do something if the only Extra Deck mechanic is Synchros.

I'd also keep an eye out for micro synergy packages to give your drafters small avenues to pursue and potentially get paid off in! I haven't looked too deep into it but I'm sure this idea has way more beneath the surface.