GamerHandle:
In short: Prestige Classes are terrible.
Huh... I always found the exact opposite in 3.5. Pathfinder is a different story, though.
In 3.5, casters almost always want to grab a full-casting PrC as early as possible and level that way (using multiple PrCs, depending on what you're going for). The design of the base casting classes is pretty terrible.
Consider the cleric. If you go into a PrC that offers turn undead and full casting, there is literally no drawback in terms of class abilities because the cleric class doesn't have any (it might screw with your BAB, saves, and HP, but those aren't generally huge considerations).
Consider the wizard. The only thing you lose by bailing out of the class for a PrC is a feat every five levels. Yeah, so terrible. The sorcerer has it even worse as they have zero class abilities after first level.
Fighters also get the short end of the stick. You get... another feat every two levels. Yay? I guess? By the time the feats start to stack up, you're probably just carrying the wizard's bags, anyway.
In fact, one of the things that extensively annoys me about 3.5 is the fact that the base classes are so terrible and the PrCs are so required.