Jumping in late on the Chronomancy discussion, it would be fun to be able to bring heroes/units/items back in time when loading an old game, spending time mana from the new timeline. For even more fun, let me spend time mana that I don't yet have to do so, getting into debt and causing all sorts of esoteric disasters. Briefly time clone enemies I'm fighting, make half my farmland intersect with the demon realm, or lock my army in stasis for a few turns.
I don't think I've ever seen necromancy done with the idea of "weak units, but no logistics trail." Give me a necromancer simulator where I'm playing cat and mouse with a kingdom that has to stand down its levies for planting and harvest, and whose knights get tired of chasing shadows. The necromancer's skeletons are technically stronger than standard kingdom infantry, but are too stupid and disorganized to win a 50-on-50 battle against fresh humans without clever pre-planning by the necromancer. The necromancer has no super units, but his armies don't have to eat or rely on a logistics train, while the kingdom's farmland is vulnerable.
Age of Wonders II: The Wizards Throne and Shadow Magic had some fun ideas with magical buildings. Late game cities have wizard towers, which expand your domain, and can be upgraded to enchant the units in them during combat, have magic turrets, and have teleport gates letting you move large armies around instantly. Your domain is the range you can cast spells in, and spreads your domain spells, like the Domain of Poison spell poisons all enemies inside.
I want to see that explored further, and with cities choosing what effects they spread, instead of the wizard. Let me build an enchanter's guild in a city to enchant 10 nearby units per turn with flaming swords for 3 turns. Or have its wizards automatically cast a Rain of Fire spell at nearby enemies every turn. Have it turn its magic towards the economy, using fire magic to smelt expensive luxury alloys for money, or terraform a nearby tundra into useful farmland for another city.
It's not esoteric magic, but outside of RPGs, it's rare enough to count: Show what it looks like when every city can have a school training wizards.