For all their flaws, I preferred prestige classes to paragon paths and epic destinies. The latter two were so fundamentally boring, nothing more than 3-4 additional powers, with none generic enough to allow you to just continue being a fighter or a wizard. When I saw some of the concepts, and how they were reduced to mechanical trivia, it really did not impress me. For instance, there was an Eladrin epic destiny, if I recall, whose highest level power was to come back from the dead by, in fact, coming from a future alternative reality, or somesuch. The rules were so concerned with making this a balanced power with other similar powers that there was no consideration of how this sort of power is an *entire* storyline in itself, reduced to a combat trick.
You can make prestige classes work. You should remove all but the most basic mechanical requirements, focusing on story-based requirements instead. Benefits of PrCs should also be less specific to individual classes, focusing instead on general usable features, indeed that needn't be mechanical at all, that complement rather than enhance a character. Allow only one prestige class per character. I would also remove them from the multiclass-level system - grant benefits on the basis of character level, not on the basis of how many levels you invest in the PrC, so that you can't optimise how many levels to take, nor when to start taking the PrC.
So for instance, to become an assassin you need to kill a specific target (or series of target) given to you by the guild. They don't care how you do it, but it must not be known who did it, or why, so any stealth or illusory abilities you have acquired as a character of whatever class will assist in qualification but not be necessary. Then, benefits granted will be based on character level, and some choice might be useful. The guild might offer you additional training in stealth (within the skill system), recipes for making special poisons (within the skill or item systems), the right to copy special spells specific to assassination (within the magic system) or, should there be a god (or other being) who likes assassination, the opportunity to petition for similar powers. If you are ever caught, the guild not only disavows you but makes you a free target for other members (what fun!).
Each prestige class would require considerably more effort than previously, more than just a 10-level chart and some rules, but I think it might be worth it. People profess a love of 2E kits: I propose we make prestige classes more like kits, only you may not get them immediately from 1st level.