Holy balls - this *is* tough.
I like the idea, taking control of the enemy - the connection to the theme wasn't clear though. It has a good in-game tutorial, but there is an extreme learning curve, and, like you've said, it needs to be balanced.
I think the multitasking nature of the game needs to be streamlined - there's a ton going on right now, it would be nice if there was a solid interface for starting research or switching control.
OR, you could simplify and focus the gameplay drastically by removing the switching-control action - the unique gameplay idea is something like a twist on a reverse-tower defense where you take control of enemy towers and stop them from hitting your dudes - or something - whatever. Point is, having all the abilities and verbs focussed on affecting the enemy would give the player a clearer metal model of what's going on.
Anyway, cool idea.