Just because Wish says you can wish for greater effects than those listed, still doesnt mean that you can do anything.
"As Limited Wish, but with fewer LIMITS"
Even there it says that Wish has limits, and it's often up to the DM to define those limits. The best way to handle Wish is to restrict it to effects similar in power to those listed. Don't punish people simply based upon wording, that's the same 2nd edition crap that was (thankfully) abandoned in 3rd edition. Only if the players are trying to be extremely ridiculous in their Wishes should they be punished. The list of effects under the spells description are all things that can be SAFELY done with wish, and should NEVER be screwed over by the DM, EVER. Only when attempting to get greater things is there any risk. When doing those things that are listed, there is no risk, period.
As far as wishing for feats, I personally would never allow it. The reason is that feats are an essential element of game balance in 3rd edition.
Why would a Wizard care about all the bonus feats a fighter gets if he could spend a mere 5000 XP for them? Why would a Sorcerer care about the bonus feats a Wizard gets? He wouldn't. Yes 5000 XP is alot, but not as much as 3 levels. Even in epic levels bonus feats are just about the only thing balancing each class with every other. Allowing people to wish for more feats completely destroys that balance.
The challenge rating of creatures assumes that they have a certain number of feats. Allowing more feats means that a character will be far too powerful for his level, especially given the exp cost. And at epic levels 5000 exp isn't very much at all, especially given that most items and epic spells cost several times that to create. And there is no sense in comparing feats to ability enhancements, as that is like comparing apples to oranges.
It is clear that Wish was never intended to grant feats, for obvious reasons. The epic level handbook also goes into depth about the wish spell and its LIMITS, and clearly the language there suggests that such blatant abuses of the spell shouldn't be allowed.
Again, wish can't do anything. It isn't an ultimate spell like it was in second edition. Mere wording is not enough to change that. If you want to allow extra feats in your game, that is up to you. But at least stop to consider what I have said, as it will unblalance your game if you do. If you don't think that the normal rules offer enough feats, then give everyone more of them, not just those with a certain spell. That's the only fair way to do it.