I'm definitely on board with this project and I definitely have some suggestions of my own.
1) If you want the maximum amount of parts in a normal playthrough you have to commit suicide and run down the clock until the boss levels are high enough to get parts. This doesn't make any sense to me and I think the bosses should be at a fixed level initially, and at a higher level in the rematch, and that's it.
2) There shouldn't be a limit on how many parts you can equip at one time. There aren't THAT many to begin with, and I think the only one that breaks the game is the jumper. That one should be removed outright. Outside of that, it's a refreshing experience to have all of the speed-boosting items equipped and it certainly alleviates the sluggish feeling that the PSX games have compared to SNES or GBA (Zero series). It's also cool to have the feeling of accumulating power through items as you go through the game (Much like in MegaMan 8 ) instead of being limited to how many you can equip.
I would almost go so far as to say that the Hyper Dash, Speedster, Quick Charge and Speed Shot should be the default gameplay settings and parts should be done away with entirely because Zero honestly doesn't need his power boosted from parts (more on that in the next point)
3) There is a huge disparity between X's and Zero's damage output and overall difficulty, as mentioned previously. Zero I feel is in a good spot but X suffers a lot in the default/Falcon armor forms (Quick Charge helps with that immensely). Meanwhile, the Gaea Armor is OP as fuck and not many people are talking about it. Sure it's slower, but thanks to the non-existent charge time you can damage bosses faster than Zero in some cases (Final Sigma) and it kind of just cheeses the game with the wall cling and the spike immunity. The Ultimate Armor has always been a cheese fest and I'd love to see it be more than just an easymode but I'm not going to be upset if it remains unchanged.
X also needs an Armorless Air-Dash and I would honestly love to see him have the float be default too, just so he's on more of an even footing with Zero in terms of the quantity of abilities.
3) I strongly disagree with decreasing the boss life bars in the rematch section; This is only MegaMan game I can think of where the bosses are harder during the rematch instead of being the exact same and I love that. It's not too bad with Zero, even armorless, and it's really just a matter of X not being up to snuff by comparison. If you must decrease those life bars I'd make the bosses more aggressive, faster, or something like that.
4) Final Sigma is my favorite Sigma in the X Games because he's so balls to the wall hard, and I really don't want him changed that much. The First form is a bit of a joke and could stand to dash around a bit faster but the last form is near-perfect in my eyes (Learning to dodge the purple cubes of death is a very rewarding experience and I'm proud to say I learned how to do it) with only a minor nitpick, that being those damn random hands, haha. Having the platform you need to stand on turn into a hazard in a split second is frustrating, because it's random and could happen at any time.
5) Whether it's the claustrophobic layouts in Izzy Glow or Squid Adler's stages, or the punishing timers on the bombs in the Skiver's stage, stages need some work here and there in X5. Not as glaringly bad as X6 but you know, lol
6) Take the X6 Z-Buster, tone down the damage a bit, give it a bit more range and that's all Zero needs here. The Z-Buster is laughable in this game, it's hard to believe it's a bonus for picking Zero at the start. Zero just needs a tool in a small amount of damage at range.
7) The bosses are generally unchallenging in this one, exceptions being Duff McWhalen and his dumb "push you into spikes" attack and I think Mattrex is in a good spot difficulty wise. Overall I think speed is just the problem.
8 ) Characters without armor take a loooot of damage and characters with armor take very little. Armor should be a small bonus instead of having such a dramatic impact, in my opinion. Zero really suffers here because he can't get armor until the endgame without cheats.
9) If you can figure out the probability of the Enigma/Shuttle success, you're a god. That shit is so fucked. I have to sacrifice my first-born son on an altar to get the Enigma to work the first time before I reload my saves ad infinitum, even with all the parts.
10) In X4, I'll take the Quad-shot buster over the Plasma shot any day. Come at me.