Well, there can still be some abuse.
I removed the channeling promotions from Luonnatar and Grigori Medics. If I didn't, then a Medic or Luonnatar turned Adept would be the equal of an archmage, without any level requirements. Cure Disease and Heal were moved to medic II and III. This also stops those medics who are randomly assigned a religion from having access to their religion's High Priest Spells. (Yes, unmodded, the Grigori are normally the only civ that can have limitless divine casters. You can summon all the Krakens/Balors/Treants you want, have Unyielding Order in every city, etc. In addition to changing the Grigori medic promotions, I made the priest spells require the appropriate state religions and made priests themselves not have state religion prereqs. I also removed channeling from all divine units, creating divine I and II instead, since I considered the Amurite Druids or High Priests Archmage equivalents (through Govannon) to be too powerful.
I removed the inquisitor promotion from Luonnatar, making a unit specific version of the inquisition spell ("Enlighten") in which the state religion of the city's owner is irrelevant. (I'm considering removing command and making the ability to capture units unit-specific too, but that would require a schema change, or have to work though python. I may also try to make the magic immunity unit specific, but, again, this would require a schema change that is still a little beyond my skill.)
I removed free promotions when upgrading arcane units. This is the biggest change. Without this, you can keep upgrading the adventurer to an adept/mage/archamge over and over again and get free promotions every time. The Hero promotion's free XP wouldn't matter much anymore, since you could get combat 1-5, heroic strength/defense 1 &2, mobility, and twincast without spending any xp, and I think that the free promotions even carried over after the spell was used (so you could get all other promotions without spending xp too).
Since they can get free spheres based on mana anyway, I didn't think the free promotions were as important anymore. I was considering increasing the mana requirements for the free promotions because I thought it would be too strong when I add lots of cross-sphere spells, but I think removing the promotions on upgrade is enough. Oh, I also made all spell sphere promotions (not just level 1) require you possess the appropriate mana.
I haven't done anything to stop the adventurers from getting free Spell Spheres, Medic 1-3, Channeling 1-3, Subdue Animal, Subdue Beast, Courage, or Dragon Slaying if they can upgrade to all the proper units. You can still have a War Chariot that can cast all archmage spells and capture multiple dragons in one turn (if you get enough mana, xp, and gold for lots of upgrades).