Funnily enough, back when 3.0e was developed, the intended purpose of those feat chains was precisely to equalise the power level between classes - what the Wizard got through additional spell levels, the Fighter would get through his feats. Of course, that didn't quite work out, partly because the feats (especially high-level feats) never went far enough, and partly because there is no good way to balance wish with "I can swing a sword really, really well."
Maybe doing feats in a way that more closely resembles spell progression would work? Let's introduce feat levels:
Feat level 0: weapon focus, toughness, skill focus, etc
Feat level 1: power attack, cleave, etc
Feat level 2: Spring attack
Feat level 3: whirlwind attack, greater cleave
Feat level 4: etc...
Every level you progress in a class that doesn't have full spell progression, you progress in the feat level track. (maybe once every three levels?). You can also retrain feats to the better variant when you have access to it.
Full spell casters should probably get even fewer feats than they get today (just like the other classes don't get free access to spells as they level up).
Regarding saves: They should probably all be level/2, but +2 for good saves, +2 for medium saves and -2 for bad saves. Fighters and such should probably get good/medium saves, while Wizards and other full casters should get medium/bad saves.