So, I like the idea that each 'tower' increases the strength of the spheres of spells that lead to it. Based on that, let's identify what makes each sphere special in question:
Elements (Air/Water/Earth/Fire) all have Tier 3 Summons. So the original idea of increasing the strength of summons makes sense, but isn't practical because of the affinity these summons already have. So, let me throw out some ideas:
1) Elementals gain the Spirit Guide Promotion. Seems too strong perhaps, so maybe something similar that gives a smaller % of XP.
2) Elementals gain City Raider 1. Roughly comparable to the existing bonus, but stacks a bit nicer.
3) Elementals get +1 Affinity in their element type.
4) Gives any caster casting a summon spell, a 10% chance to twin cast the summon. This could be a bit of fun random power, and definitely a bit more unique.
Okay, so what about Alteration? (Nature, body, life, enchantment). Tier 3 is a mish mash. We have a bit of teraforming, a bit of support. Yikes. In fact, none of these even include a resistable spell to begin with, so maybe it's a good thing we are changing it. All of these, however, have some pretty potent unit based effects. Nature and Enchantment both pump a class of unit. Body has both haste and Regen, life has ress. So something focusing on making units stronger would make sense. Some thoughts:
1) Your units heal 10% after any successful combat.
2) Allows your units to take the "Altered" promotion, which requires Magic resistance. It gives +1 Movement and +20% attack strength.
3) All units built in the city with the Tower have +6 XP, and Recon Units get Poisoned Blade automatically, and Archers gain Flame Arrows automatically.
4) All units built in your empire start with a "Mystic Concoction" promotion, that gives them the ability to "Drink" the concoction to regain all Health, and gain +15% strength for 1 turn.
5) The tower does nothing but grant +10 Great Commander Points.