Ugh, yes. This is one of the things I really, really hate about the elaborate prerequisite systems in 3.5E--not just for prestige classes, but often for feats as well. It's like somebody deliberately sat down to craft a system that would crush all the vitality and personality out of player characters and reduce them to a lot of numbers on a page.
It's not that PrCs in and of themselves hinder roleplaying. In fact, they have the potential to enhance it. But when you have to plan your character from day one to reach the PrC, and take a slew of feats and skills that have nothing to do with your character concept, it's death to character development.
(For me, at least, it also sucks the joy out of levelling up. Instead of a broad vista of possibility opening before me as I contemplate my choices for the new level, it's just another step on a road I already know from beginning to end.)
PrCs should have at most one or two prereqs, and those should be no-brainers that anyone going into that PrC would naturally have. It's fine to require Two-Weapon Fighting if you're going into the Tempest PrC, or to require arcane spellcasting if you want to become an Archmage, or sneak attack for an Assassin. But one should never balance a PrC by requiring bizarre, irrelevant feats or weird skill allocations.
I really hope there aren't any prerequisites for paragon paths and epic destinies in 4E (or if there are, they're no-brainers as above).