This post is really surprising to me because I know your an avid pnp player.. and I couldn't disagree more.
Do you avoid power builds or something? Or just don't play 3.5E that much?
tl;dr: IMO the tightly-specced prestige classes are even worse for tabletop gaming than cRPGs. Tabletop gaming is even more about player creativity, and having to build to a tight template feels really suffocating.
Longer answer:
My two longest-running campaigns were AD&D and D&D3, respectively. Neither of these was all that combat-heavy; the focus was on exploration, discovery, and role-playing, although we did have a fight about every other session or so. We got to around level 15-18 on both of these; the campaigns ran for several years real time. In these campaigns, there was only one player who was really at all interested in character-building; everybody else was more or less just rolling with it. We had a lot of fun working a fair bunch of modules and settings into the larger framework of each campaign. The rules were more for flavour and to give a bit of structure and a sense of mechanical progression, and D&D worked fine for that purpose.
Then I ran a shorter campaign with a slightly different group; here I had three players who were NWN veterans and genuinely into powerbuilding. We also had a ton of supplements on the table, so there really was a wide range of PrCs to choose from. I think one of these three got a kick out of it; he planned out his entire character development from the start so he could hit his desired PrC as early as possible, and then, well, coloured meticulously inside the lines. But then I think he wasn't entirely neurotypical, so he got a kick out of that thing. The other two had much less fun as the concepts they actually wanted to play weren't really quite like the PrCs they were after, so we ended up doing a lot of negotiation to tune them to spec, and ended up houseruling a fair bit, which then made the third guy who did follow the rules to the letter a little upset.
I as the DM didn't enjoy it nearly as much; a lot more energy was spent negotiating rules and exceptions to the rules and just focusing on the rules and making sure the right feats and skills were picked on leveling up and such, and much less in-game. Overall I and most of the group felt that the system didn't really work all that well; the PrCs were sort of cool but they were somebody else's cool, and there really wasn't much room for player or even DM creativity there.
Fiiiinally, in my view the whole notion of power building is kind of irrelevant in a PnP game anyway. With a human DM on the other side of the table, raw party power is kind of irrelevant; there are always creative ways to approach challenges (or run away from them, or recover from nearly total party wipes), and managing the challenge level so that things stay interesting is the DM's job, and a reasonably good human DM will always be able to do that better than an algorithm. From the DM's PoV it doesn't matter if the party are powerbuilding veterans who know the rules, use them to their advantage, and prep carefully, or role-playing geeks who are in it for the story and the adventure and the excitement -- or level 1, 10, or 20. In all cases his job is to toss fun challenges at them, riff off them when they respond to them, and do his best that everybody's having fun. Only the specifics of each challenge matter.
Summa summarum, no I don't like PrCs for PnP either, worse in fact than cRPGs, as PnP gaming really puts player and DM creativity front and centre, whereas tightly-specced PrCs take that creativity away from them and put it in the hands of the people who want to sell you another Complete Book of Elves.