I like how the base clases choose options as they level up. Then I had my brain pull one of its 'fuzzy' moments, and had an idea.
I was thinking that Barbarian and Ranger were just fighters with different feat types. (Especially ranger, putting terrain and FE in place of armor and weapons.) Somehow, that got mingled in with PrCs (prestige classes).
It hit me; PrCs are just optional picks with specific prerequisites. Once you meet prestige class requirements, then the new pick options start showing up. So you're still a level X main character class, just with options not available to the plain vanilla, who is still better at the mainline stuff than you are.
I would also sever specific organizations from a prestige class of the same name. To grab Hellknights from another thread, I can make cases for base classes of all four archetypes. Rng. PrC choices need a little more work, since different base classes will be taking them. Other than that, it's just a matter of mapping out the 'branches' of ability.
I'm tempted to bring the discussion of Pools from Iron Heroes into the open, but I'll leave that for someone else. Where I would be heading with that is that multiple sources can contribute to the same 'PrC type-level' for the purposes of abilities based on PrC level. For example, Moon Clan Ninja and Kensai would both pull off 'ki' level for their effects, determined by the number of picks from their options.
Ooh, evil, evil thoughts... I'll stop typing and go read somewhere else. This idea still has momentum, and if I keep typing it'll eventually end up in a place where nobody else will want to contribute.