Well, I've always given fighters 4+int skill points, any two skills as class skills, and every other feat (2/6/10/14/18) as Wildcard Feats (see below). Maybe changing all the Fighter Bonus Feats to Wildcard feats, as well as the extra skill stuff, would make them worthwhile. The Wildcard Feats alone may actually do it, as they're a pretty cool unique ability, representing a very broad area of training expertise.
[sblock=Wildcard Feats]I got the idea from the Iron Heroes book, but thought the 1/day part was a little stiff.
Basically, certain Bonus Feats* become Wild Card Feats. They are left blank. At any time, you may concentrate for one full round. If you do, you may choose any Fighter Bonus Feat you qualify for, and this feat fills the Wild Card Feat slot. The feat is 'learned' until you use another Full Round action to 'learn' a different one. If you use this ability to learn a feat that grants extra HP and later trade that feat for a different one, you lose the HP that was granted by the feat, as if it were gained through a Con increase.
* All of them, in the case of the E6 Fighter.[/sblock]That was an old house rule of mine, and I completely forgot about it for this. It seems like it would work, an Wildcard Feats are a very good reason to stay full Fighter.