This is what I do and it seems to go over pretty well with my group.
I review all the rewards and count the number of skill, power and card feats. Then I look over a few character cards and get a general idea of how many check boxes there are for the three feats. Skills are typically 15 across the board for all characters and I think card feats are around 10...? but power feat boxes may vary a little.
So say I have 15 skill feats on the character card, and the rewards from the entire adventure path give us 11 skill feats to earn. I'll start all the characters with 2 or 3 skill feats right off the bat.
It doesn't over power characters. (One might think it does but not really.)
It still leaves us with the inability to max out on all the skills by the end of the adventure path. Or in some cases we will still have skills that never receive a bonus.
So for instance with the Wrath set, I'll allow everyone to start with one power feat, one card feat and three skill feats.
Again, it doesn't overpower our characters and we don't feel like putzes from the start. And it does help curb the feeling that the existing feat rewards are limiting.