Model magic somewhat after the research tree, where the casters gain levels and choose perks to unlock higher echelons of magic, and then give them points to spend CHOOSING spells from the trees they have access to. Want to be a largely civics-oriented empire, and win via alliances? Spend your spell points buying city enchants. Want to be an out-in-the-field tactical warlord sovereign? Forget mana for cities; Focus on buying new ways to light people on fire! Let us see from turn 1 what sort of spells we have to CHOOSE from in an interface, and let us PLAN on how we want to develop. Let us be excited for our next champion level so we can get more points to spend on spells... Or not.
Choosing spells you want to have access to seems to be the ticket. It should really be in the "tech tree" but that doesnt seem to be keyed to your heroes...
Though in a sense you already do that since you select spell paths such as Fire archmage.
Another idea i suppose would be to retain the fire-water-earth-air-life-death but change it such that you don't get everything in the path.
Say there are 12 Fire I spells, 12 Fire II, 12 Fire III, 12 Fire IV and 12 Fire V spells
Even if you start off with Fire apprentice, you don't get all 12, but maybe you get to pick only 4 of them.
Fire apprentice -4 Fire I
Fire disciple - 6 Fire I, 4 Fire II
Fire mage - 8 Fire I, 6 Fire II, 4 Fire III
Fire master - 10 Fire I, 8 Fire II, 6 Fire III, 4 Fire IV
Fire archmage - 12 Fire II, 10 Fire III, 8 Fire III, 6 Fire IV, 4 Fire V
Spell progression is still not research based like MOM but XP levelling based. But at least (1) is keyed to champions (2) There is some forced choice.
If you want to make it more complicated, it can be random.
e.g Your champion is now A Fire mage, he has learnt Feedback, Mantle of Fire and Wall of Fire. Or maybe some trait would allow you to select instead of random...
I suppose having more magic related paths which give different bonuses and spells after path of mage will help.
Path of Summoner - obvious, stronger summons, more summon options
Path of Invoker - strenthens direct damage spells, more of such spells
Path of metamage - spells that counter/interrupt/dispel/anti-magic
Path of artifier - creates artifacts
Path of enchanter - bluffs postive and negative, making them harder to resist etc
Path of Necromancy - prequisites are death mage...
But really these should be choices by the soverign at the start and in a way compete with the whole element system already in place.
When you raise a level, you can sometimes choose as a bonus to gain an additional spell instead.