the problem with eliminating PrCs and replacing their abilities with feats is 2 fold:
1) A character doesn't get enough feats to make things work that well (you've partially addressed this by giving more feats, but...)
2) Many PrC class abilities are much more powerful than feats.
Most feats are pretty underpowered and boring, actually.
If you were to spice up the feat selection to include PrC abilities, than you might get the danger of having the players select the interesting PrC ability-feats and leave the core feats fairly untouched.
So there's 2 potential dangers:
--Too powerful of PC's since they've got more feats, and they've selected the cream of the crop of PrC-ability-feats (and they didn't sacrifice anything to get those PrC abilities).
--Too weak of PC's because you may have to water down the powerful PrC abilities too much, leaving them with only a couple more feats than a normal character, but they'd have to spend a LOT of feats to make something interesting and effective.
Really, I'd just deal with the beast and allow PrC's, carefully checked by you.
They won't probably be asked about for QUITE a while, if you start low level, and the players are new to 3E.