Perhaps one could consider the Tower of Elements affecting the damage caps of spells of those elements?
Perhaps Tower of Divination should have a cap at a number of research points (like a great person does), to reduce its power to be closer to the other towers?
@Marchwik-
The old Tower of Alteration was more effective (it worked through 0.24, to my recollection), so it wasn't too bad for armies of mostly mages and/or (offensive) priests, but I'd agree that it was never the best tower.
I think you underestimate the power of Skeletons or a Necromantic strategy, probably because you apparently aren't used to using large numbers of mages to summon hordes of undead to do your combat for you. Simply put, enough summons can take out nearly anything, and at a very small cost to you. Significant numbers of Death affinity units alone can make the Tower of Necromancy worthwhile.