I just started playing this beta yesterday, and I have to agree the magic system is clunky.
So far I have used it very little (summoned one thing) because of it's inaccessibility.
First in my mind is the organization, it seems somewhat random and cluttered - all of the spells.
I would like to see them more clearly organized, maybe give the option to organize by spell level to see all of the new spells available after you've researched a new level.
If a spell takes a special kind of magic/shardthing to cast, I would make it so that it requires that to research as well. At first it was confusing to research a whole bunch of spells and try to figure out why I couldn't cast them - especially when there were no corresponding shards on the map that I could find, I thought I had to be doing something wrong which was frustrating.
Maybe a little tool tip or pop up that tells you "you can't cast this because you don't have enough X" instead of just having them crossed out.
It also seems more confusing and tough because a lot of times when you build your own character and specialize in only one magic school, it is luck of the draw to have one near you that you can actually use, especially when you're playing on a map with multiple continents or islands.
It can easily be more than half the game before you can cast something, which doesn't seem right for a game based on a war of magic.
Maybe have more spells (up to level 10) that you can cast with just normal manna and not rely on any shards or anything?
Like I mentioned I just started yesterday, and have tried to play about 8 games, none of which I have been able to finish yet, so I apologize if my info is wrong - this is just my impression of the spell system so far.
Hard to use, somewhat confusing, not all that useful compared to building a large upgraded army.