Well you´re rigth, prestige classes should be more for NPCs use.
I really like the simple multiclass system with the really cool "variant rules"
But i think that there would be some space for Prestige as PCs, but they would have to represent really special groups, martial, civilian or sorcerous that can´t be really defined by actual multiclass, and that carryed real roleplay restrictions with it, like the priest feat has.
I actually don´t use them... and if i do, there will be a restricted number of prestige classes, one for each race/sub-race, or specific a kingdom...