The point is that fighters become even more pointless with E6. Early on, you get some cool feats and such, which almost makes up for all of the unique abilities and class features that other classes get. After 6th level, though, everybody else is taking all the same feats that you have, since there are only so many to take, and you get so many. Very soon, the fighter's bonus feats become completely outstripped by the bonus feats that everybody gets after 6th level.
There's no real reason to play a fighter unless you're just dipping, or you know the game won't get far past that 6th level mark. Which is alright, I guess, as there are plenty of fighter-like classes that can take the primary melee place. But I was just trying to make a way to keep the fighter while making it still viable to play.
Alright, how about this: every 2500xp, a 6th level fighter can trade a single feat he has for any other feat he meets the prerequisites for. You can't trade away a feat that is a requirement for another feat you have, however.
This allows the fighter an extra bit of versatility, allowing them to remove feats that are useless later on. And, if they hear early on about an enemy, then gain some xp on teh way to fight them, they can "retrain" to better combat that particular foe when they get there.
Edit: Crosspost. I see your point, I guess. I'll just use that in my own E6 game, then. Once I get it running...