I like prestige classes, but I prefer custom designed ones. If I'm playing and looking through books for a concept, I am not using my imagination as much as if I were simply dreaming up a concept whole cloth. That may seem like extra work, but the DMGII offers good guidelines for creation.
IMV, only the Rogue, Fighter, Cleric, and Wizard are core classes anyways. To be core they have to be generic and customizable on their own. They're archetypes. Additional classes, whether 20 levels, ten, five, or even short classes that start at Character Level 1, are all Prestige Classes because they are specific. This means the classes themselves have setting roles. Barbarians, as RAW, are only one type of many wildmen in the setting. Class variations, like in UA, allow for expansion to reflect different cultures, but in truth they are all just PrCs based off Fighters.
So, for me, the narrow-benefit for broad-penalty optimization of PrC classes is mitigated by requiring in-game justification. PrCs are made jointly by player and DM with setting rationales in place throughout.
While I like the very expansive number of character options PrCs allow, they do cause one problem for me as a DM. They mean no unique NPC can easily be dropped in a game without a ready prepped PrC to back up their unusual powers. That's much harder than older editions where classes were almost always mechanically the same, but descriptions allowed variations limited only by imagination. Setting justifications were needed, but not necessarily mechanical ones. (they have the power because it makes sense in the world and they have the archetype class) Because I create my own PrCs, I can come up with mechanical justifications after the fact. It's just time consuming.
