3e had prestige classes, but my experience with those was that most prestige classes were not so much “choices at higher levels” but rather “something to plan from level 1” in order to meet the prerequisites in reasonable time.
I think 3E's prestige class was a good idea that went wrong. In the original core, it was more presented as a world building tool for DMs. Create a prestige class to represent something special in your world, and then present it to the players at some point in the campaign as an optional path they can multiclass into. In that capacity, it was a good evolution of D&D design, IMO. Unfortunately (or fortunately for the CharOp advocates, I suppose), it didn't take long for future books to turn it into a purely player facing building block, and a source of significant power creep in the edition. And of course, as you pointed out, it also went from being
an option to
the option that directed players' other character building choices.
I think if I was to redesign the concept, it would be closer to 2E's kits, but more consistently designed, and something a player can take at levels other than level 1. Make it something of a rider the DM can optionally present, and the player can optionally accept. Doesn't take up space in the main progression system like prestige classes did, and doesn't lock you into anything for future progression like subclasses do.
Combine that with
my other post, and increase the rate at which feats are gained (in my 10 level setup, I'd go so far as giving one per level), and you'd have a progression system where players constantly have progression choices to make, and the DM has tools to give avenues for the player to do so in a way that fits into their campaign world.
