I did, indeed, work on a similar project a while back, but with a key distinction-- I used the more-balanced M&M as my base, and modeled classic D&D abilities using its rules; you seem to be taking the less balanced 3.5 and trying to import... some point-buy rules, but not all. You're still buying haphazard level-based abilities, you're still allowing uncapped bonuses, and... as noob noted, your costs are already out-of-whack, even before you get to unquantifiable special abilities. Like, as far as I can tell, just the Barbarian chassis would be 7 pts/level.
If you want something that's close to being in between the two systems, maybe take a look at True20? It's another Green Ronin game, a more point-buy version of the 3e paradigm, and it has a custom class creation system.
*Ish. Provided no-one tries to hard to break things. But it's obvious when you're doing it, and it's not something that's restricted to certain character types.