Treat Zero as a special weapon of sorts.
Damn my perverted mind!

As for X3, yeah I think that it had some issue I'd probably resolve too. First off, I agree that Zero would have been better if Playable after you beat the game. Heh, they could even reverse the role in the opening stage, except that X doesn't have Zero's kick ass theme. Speaking of Zero's theme, give it the Vile MHX route where it just comes on every [tornado fang]ing level you play. Yeah, that theme is just that bad-ass in the eyes and ears of Protoman Blues. Also, make it where you can swap out Zero for DomincanZero. Why? Why the [tornado fang] not? This is MY dream X3 game!
As for music, I actually have no real issue with it, except for a few tracks. Those tracks are namely Blizzard Buffalo (still my least favorite X song ever), the Boss Battle, Dr. Doppler Stage 2 (I [tornado fang]ing LOVE DOPPLER STAGE 1), and Dr. Doppler's fight theme. Dr. Light's theme was pretty weak too. Other than those, I thought it had a decent soundtrack.
Weapons, yeah the weapons were kinda meh. Cool ideas, just not executed in the best manner. I still do love giant spinning Slashy Death Yo-Yo though! As for the Buster, it's a step down from X2's Buster, but then every buster is in my eyes!
I think that's about it. Overall I still do love playing X3 though. Yeah, I like X1 & X2 more, in terms of SNES X games, but I still do like it.
Oh yeah, one more complaint... WAY TOO MANY [tornado fang]ing DOORS.