One thing I would like to see (since you mentioned MtG and took some concepts from it) are counter spells and a casting time for certain larger spells.
Though I still fear that the spell system is going to suffer the fatal flaw of only a few really good spells which will wind up the only one's ever reseached/gained and then cast.
I think that some mechanism need be added to make that less of the case. Weather it's restricting available spells (randomly or otherwise, but some way to keep people from using the same over and over) or granting bonuses for certain spells based off of casting location (think Dominions where you could find sites that reduced the mana cost for various schools).
I do understand the desire to put in these mega spells, but clearly if you make them too easy to use they will rule the game, too hard and they become near meaningless. Especially if you cannot use them until near the late game when often times the outcome may well have been decided, moreso if magic power is tied to general empire size/power.
There really needs to be a guns or butter or spells tradeoff I think, and the easiest way to do that is to tie the sovriegn's actions directly to those choices in such a way that one cannot manage all 3 (or probably even 2) in a single game.
