I wouldn't mind if Combat feats and non-Combat feats were totally separated. I want the combat feats to be bad-assed as hell, and for you not to get many of them (unless you're a fighter). But I understand if you want some just because they're cool. So why not have two separate pools of them, and two different sets of slots to buy them with?
Of course... that's starting to sound kind of like 2nd edition.
Nah I think one pool of feats are good enough really, the thing is to make interesting enough feats for everyone that they have to waver on what feat to take each time they take a feat.
For example
(Twf is my favorte example cause everone see the progression easily)
You get Twf, Itwf, something that lessens two weapon fighting penalties... like the tempest does, then, Gtwf
all keyed to base attack bonus
All for one feat. Thats great for any melee-ist as well as good for the fighter if all things are taken equal.
Then you have rage feats... For example... uhm...
Burining Rage: Pre-req Barbarian X (in some capacity tied to barbarian level)
Your rage explodes forth as a blistering flame When you enter a rage all creatures withing 20feet must make a reflex save 10 + con + 1/2 char level or take 1d6 fire damage per level Save for 1/2. They must also make a fortitude save or be knocked prone from force.
Finally for the duration of your rage anyone struck by one of your melee attacks catches fire as desribed in the dmg
Now thats an example of the other type of feat. There'll be combat feats that give new abilities and "Class ability feats" that enhance existing options.
and maybe a few more. That makes things about equal with taking metamagic.