Hm. For some reason I suddenly feel like I should see if command mission is any good. Maybe a turn-based structure could make boss weapons worthwhile again.
Megaman as a robot mage-type? It could work.
Unfortunately, Command Mission doesn't really bring boss weapons into play other than
why are you still showing up in games Axl using his copy ability to duplicate a boss' big (non-)elemental (still just Fire, Ice/Water and Lightning!) attack.
It's a pretty vanilla RPG all things considered, but I'm guessing it was more of an experiment on the X7 production team's part than anything. There's a lot they could do with it if they decided to make sequel though. While I'm dreaming, I would like a new Breath of Fire game that is a mixture of 3 (I love the dragon gene system goddamn) and 4 (because I loved the visuals) while forgetting Dragon Quarter exists.
Edit: Contributing to the topic! I'm looking forward to The Last Remnant next month and Valkyria Chronicles so I finally have something to play on my PS3 that isn't MGS4.