I agree with you that some of the PrCs are probably unbalanced, but I don't see that as a high priority "have to be fixed"-problem. One needs an approval to take a PrC so I feel that they are more like role-play classes than "make your character stronger"-classes. If one wants to make a strong character, go for the base classes only (fighter/rogue?). On the other hand, if one wants a more unique character but don't mind it to be weaker, pick a PrC. It's one's own choice.