To me, prestige classes are an overcomplication. They work rules-wise, but in a complex system, I think it is better to remove any rules that incrementally increase character types instead of exponentially increasing them. I have never come across a character concept that I can't create using 1-2 standard classes, plus background and flavour.
What I would like to see, for things that might get a prestige class, is instead a couple of manuvers, equipment, spells and feats, all thematically linked to the topic being covered, so that I can select things that make my character more like the topic, without it overriding aspects of core classes. So if I'm making an adventuring entomologist or whatever, then maybe I can get some bug-catching equipment, a feat that gives me +1 to a stat and a range of bug-related abilities, and a locate bug spell, or a maneuver that allows swiping tiny sized creatures from the air and into a cage.