I don't know that classes and themes and more racial options totally knocks out the room for prestige classes (and paragon paths, and the like). RCT may not kill prestige classes and take their stuff, but they probably do mug them, take their loose change and credit cards, and leave them standing on the corner rather disheveled.
Time you get rid of prestige classes that are nothing but alternate flavor with a handful of mechanics, or bad choices for what should have been more or better classes, then I don't know what is left.
I guess I could see a hybrid prestige class/paragon path setup--if classes were deliberately kept short and sweet. Say, there are 20 levels, but core classes only have 10. (Or 30 levels, with core stopped at 20, or whatever.) Then you might reach a point where specialization at the upper end was better reflected by a handful of prestige/paragon classes that were mutually exclusive, rather than extending the core classes with a proliferation of options. I doubt it, practically speaking, but I can see circumstances where that might be true.