Yes and no. I occasionally "regret" that a feat did not exist when my character could have, and probably would have, wanted it most. But I don't think the ever-increasing selection of feats (and/or PrCs) is bad in and of itself.
Feats: More feats means each character can be a little more unique. If you are agonizing over which to take, that is a sign that those feats (or feat-chains) are fairly well balanced (as in equally desirable). I know players who like to min-max, and they have a love/hate relationship with new books. They love them for more ways to tweak a character, but they hate them because they can't have it all in one character. These people also exhibit the (IMHO mistaken) belief or assumption that you're supposed to be able to "get 'em all" for one character.
PrCs: This one is harder for me to justify. There are three main types of PrCs -- mechanic fixers/exploiters, organization members, and niche roles. To be valuable, the PrC either has to be nearly-flavorless (mechanic fixer/exploiter) and the DM has to add it all for his/her world, or has to have a flavor that is adaptable to any world (niche roles and organization members). Of the ones that need to be adaptable, many aren't. The Red Wizard of Thay and the Thayan Knight are two examples of classes that *probably* should stay in FR. IMHO, a DM is better served looking at them as models and making his/her own organizational PrCs for his/her world than trying to adapt them to fit. However, I still consider such PrCs good for inspiration. When Sword & Fist came out, I sort-of liked the Cavalier and sort-of liked the Warmaster, but was not really overwhelmed with either. So, I made my own -- the Noble Knight, which had moderately high requirements to enter, and mixed some of the Cavalier's horsemanship with the warmaster's troop leadership. And it was "just right" for my world.