Darn. I wish I could think of some good upgrades about now. Maybe some stuff to apply to the Limit breakers. That's the only thing I can think of. But, that's kinda hard, because it would have effects and make the game too easy.
Here's one. Increase the effects of items. If you haven't already.
SS4FlameAlchemist
You need to be able to switch armors like in Command Mission. They each had armors that they could use. Maybe use two of any of X's armors, possibly Dark Zero, absolute zero, Omega Zero, or even Nightmare Zero. And for Axl, He could have a stealth mode, and His white armor from X8. Just some ideas. Watch some Command Mission videos or something. The transformation system from that game would pretty much fit right in with this. Anyway, just rambling now.