I have a suggestion that I haven't seen implemented in other games, which is prerequisite units or buildings for research. Well, I've seen prereq buildings, but not units.
In a PBM game I used to play your mages could either study a new level or do stuff in the field. The opportunity cost of advancing your magic was not using the magician himself while you were doing that research. I'd love to see a little of that in the Spell research tree (or Tech as well, if it makes sense). You can't research how to enchant weapons, or brew potions without having trained an alchemist or enchanter and stuffed him to work in the building.
I like the idea of tying people to the research rather than having advancements being more abstractly researched. This actually dovetails to some extent with the concept of heroes, but more like key personnel. Does that blacksmith stay at home and churn out stuff, does he team up with the alchemist to help research how to enchant weapons, or does he go off with the army to give an advantage there (maybe better weapons maintenance or some such).
That might create a usability issue though if you've got too many key personnel to handle, but it was quite a bit of fun in the PBM game to agonize over whether I needed that wizard's power now or to let him study to get even more powerful for later.