One other way I thought of for Progessive tree, that might be a bit different is:
1) At apprentice level make a resource appear for each skill (so at the more expensive apprentice tech of Alteration; the Alteration resource becomes available)... Now the Adept, Expert, and Master buildings/creatures will require the Alteration resource to be able to be built.
These techs won't be required to advance, and flavors can make some civ's 'maybe' research them (25, 50, or 75% flav), some civ's always research certain ones (100% flav), and some civs never (0% flav).
So you can somewhat control it to a certain extent as the tech tree progresses. Down the line, a civ might research master, but can't use it until it gets the resource. That early apprentice tech would have to be fairly expensive (so down the line it can't be researched in 4 turns / make it a forced 40-turner).
But in this case, it would require about 18 resources to make it work, one for each skill. Might be too many? Would only leave 14 resources for everything else.