With mana being changed to a global resource for your Kingdom rather than a per unit resource I see this as creating a new opportunity for unit customisation.
Certain Magical techs could unlock direct unit modifications that would cost mana as a resource and grant special abilities sometimes with an associated visual effect on the unit. These modifications could be on armour (rock like skin), Weapons (claws), Other (Regeneration). The point is that as Mana is now a kingdom resource it could be spent just as gold or materials could.
Likewise stardock could add a weapon forge and have magical technologies that also allow the player to design magical effects into weapons giving them a mana cost when added to a unit.
This leads me on to another point now Mana is going to be a kingdom resource pool, crystals (for making magical items) are redundant and should be removed, they exist just to give a resource needed to forge magical weapons and objects and that can now be mana, which is more interesting because you have to balance your spell casting with enchantment and imbuing. It also means you don’t need to find a rare resource to exploit any sort of objects build able form the magic tech path.
As far as flavour and story is concerned I think Empires should get more and better Magic unit mutation techs since direct mutations of their people is more in keeping with the very ethos that created the fallen to start with and kingdoms would tend away from it. Magical forging e.g. creating magical items should there for be stronger for the Kingdoms.
What do you think?