Thanks for the detailed reply.
But this
makes me sad. I think the 3.0 PrCs are the best part of that game. I mean, not the combat monster broken ones, but the ones that are part of the setting and are there to talk about the character's place in the world.
One of these days I am going to bring them back to 5E.
I love the idea of PrC's as Monte Cook outlined them, as being representatives of secret orders within his culture and a way of establishing complex cultural ideas and giving players a sense of attachment to the world. The trouble is that PrC's that did that largely did not exist and were largely never published.
Instead, PrC's became a whole of bunch of different competing ideas fulfilling a bunch of different theoretical roles, but largely printed as filler content to ensure each book would meet the brand manager's desire that all books be both player and DM books (to encourage players to buy more books for CharOp reasons). Gradually, the PrCs started looking more and more like "push cards" in MtG sets, where the brand manager knew the cards were under costed in order to push them into the forefront of the meta and encourage excited purchases because of the power creep.
But in terms of purpose in the game they were all over the place. Some of them existed to fix holes in the class design (such as Paladins only being good or Barbarians only being chaotic wilderness dwellers). Some of them existed to fix holes in the multiclassing (multiclassing into a spellcasting class is never good because the lost caster levels are never as good as the marginal increases in skills or BAB). Some of them existed to fix holes in the Feat trees where the feat trees didn't provide for a particular concept or where the concept would have been weak and unattractive without a power boost. Originally, they weren't necessarily better than standard classes, but a lot of them ended up being basically a base class plus a bonus feat every level which was strictly better than base classes while breaking the games design since instead of choosing like a feat you were locked into a rigid progression. But the worst thing they did was exempt PrCs from the multiclassing mechanics, which mean that what they became in practice was overpowered feat selection. Most of them were very front loaded to do their thing, and as the number of PrCs increased more and more of them had the same focus - multiple PrCs for archers for example. So you could select a PrC like a powerful feat, and stack more and more bonuses to the same action on the character. This was at its worst when the base class being modified was already Tier 1 and the thing it was doing was already powerful.
I can't imagine me bringing them back because I consider them the worst thing about 3e and the source of 50% of people's trouble with 3.5e (much of the rest is OP spells and badly designed saving throw scaling). But if I did bring them back I'd make the requirements for getting into them so harsh that no one would be able to plan a build around them and I would not exempt them from the multiclassing restrictions. So for example, I could imagine a PrC like, "Dynastic Ruler" whose requirements were you must become a sovereign by your own hand and produce a legitimate heir before you could take levels in the class. A lot of that overlaps my own ideas for "Epic" level play that I've never really written down because I can't imagine me running a game that makes it to 20th level.
One of my own players who came from a 3.5 background felt something like you did until he played with my rules a while and one day he'd been making characters on his own (because he loved designing characters), and his eyes were bright and he said, "I just figured it out. Under your rules, characters don't take prestige classes, they become prestige classes." That's basically the idea.