Ideas and suggestions.

for example, make Town Portal water magic. then in the late game water will be necessary, and earth won't suffer, since it's still imbalanced because of slow. (as an option, swap prayer and Town Portal)

Mass Prayer is not that much worse than Mass Slow, in my humble opinion.
And in general... When you start dividing utility between the global map and the battlefield, balance becomes very hard to find, maybe even impossible. In any case, the school that allows fast movement will be a must have, while the others, even if their value increases, will still be some kind of "add-ons".

in addition, make the 5th level of fire immune to cube, i.e. implosion and fire elementals will still work, this would be some kind of balance between mages and Knights. to avoid making mages imbalanced, you could ban magic in the case of the cloak and the cube.

In my opinion, this scheme is an order of magnitude more artificial than the ideas in this thread regarding new spells on the global map.

p.s. forbid Logistics heroes from water magic, Gunnar can't take it anyway as far as I know, this would somehow fix the Logistics specialists. (let the noob with water run around and send Gunnar home, why not)

Again, complication. What's wrong with simply adding a new spell to water? Well, okay, maybe not "simply," but at least you wouldn't have to shuffle spells (which, in my opinion, even contradicts the idea of this mod, although I can't guarantee I'm right about that. But the fact is that such a change to the "old" setup will surely have many opponents.); introduce tricky formulas about which artifacts forbid what and what they don't; forbid things for Logistics heroes...