Perhaps, and I'm totally going off the cuff here, a combination of "Themes" (since I understand they will add some Skills to the PC) and a, sort of, kinda, maybe, "Talent trees" set up...built in?
At first level you would take, for example purposes only -I would recommend at lest 2 or 3 separate ones per base class (Cle/Fte/MU/Thf) or, at least, based on your base class (so a Druid could choose from Cle Themes, Rangers from Ftr, etc.)...
But let's say, for this lil' mental exercise I'm working out as I go, that a 1st level Magic-user takes the "Apprentice" theme.
At level 3 you would, automatically move on to:
Herbalist OR "Special [Arcane] Interest".
At level 5, the Herbalist theme transitions to "Potion-maker" or something like that or "Local Witch"...or can choose a separate starting (level 1) Theme.
The Specialist theme transitions to "Expert [Arcane Interest -whatever the PC chooses that to be], ...or, again, chooses some other level 1 theme to begin.
At 7th, the "Potion-maker" goes on to full-fledged "Alchemist." The "Local Witch" goes on to "Noted Oracle" or some such...
The "Expert" goes on to "Sage."
And that tops out your theme. You can start up a different one...or maybe, for an "epic level" supplement/expansion play you could develop "Master Alchemist" or "Sage-Savant" or some such.
They aren't things that you need to "take" or spend "feats"/"skill points"/resources on they just transition/increase in knowledge and power (additional skills) as the Player chooses as their PC increases in level.
Still and yes, we really need to know how they will work/what they will entail to come up with a plausible list of options.
But the more I read and think about them, the less I would want them to be additional/sub-/prestige class add-ons. Leave "class" abilities to increasing "Class" level. Themes should be separate, sometimes useful, skills (mostly "non-combat" oriented if I could chose) but not "character power" defining, per se.
Again, as per usual these days, just typin' out loud. haha.
Have fun and happy gaming, to all.
--SD