There are lots of issues with the spell system but those are already being discussed elsewhere.  What I haven't seen mentioned yet though is the use of the term "spell points".  In many games spell points are just another name for mana.  In your game they are basically spell research points.  With having 3 magic terms already I think it is important for them to be pretty clear what they are right away from just the name.  I think having spell points and mana mean two different things is a mistake.  I've been playing strategy games and rpgs for as long as I can remember and I found this confusing initially.  I have a feeling once this gets released to fresh eyes you will find a number of people getting confused with this also (if only for a short time).