I think all forms of buying feats should not be allowed, including flaws. I also think feats shouldn't suck, but that's a much bigger issue...
Well until fixes like what you did in Exiled start to apply money really does = power in D&D. I would love to disconnect the standard economy from items that give your character real power, which would include feats and magical items for the most part.
Yes, at it's core this is a problem with the D&D economy more than it is with feats. But the fact that most feats just flat out suck, but some are awesome, and that PrCs and other feats use prerequisite feats as a "tax" to make you waste valuable character resources on junk, both annoy the crap out of me.
I think feats need to be equalized, especially the ones for non-casters. Most of them are just utter garbage. If you improve them overall, then you certainly shouldn't put a way in the game to get more of them cheaply (i.e. flaws in a Tome game).
But then again, there are already insanely powerful feats in the game like Persistent Spell, Divine Metamagic, and Planar Touchstone. Obviously letting people buy those feats is a bad idea (at least IMO). If those feats aren't banned, even letting them buy other feats is a bad idea, since it lets them get those feats earlier than they would have without it.
So, in summary, letting people buy feats is a bad idea, no matter what, except for feats that just plain suck, and even then it's only OK if they aren't being used to let someone make a power grab (i.e. buy Iron Will so they can get to Incantatrix 3 and start Persisting their whole party's spells immediately... like my wizard in Amechra's game will be doing.
). If they're just buying Iron Will for a +2 to Will saves, go ahead. But who's going to do that?