So, After running through the first 3 missions (which were awesome, no complaints thus far), I've accumulated all these skulls, and I decide that I'm going to see what the hell they're about. Go to the elites tab.....and I'm utterly lost.
Now, after about 10 minutes of messing around, I figure out that for each faction you're allowed to have 3 elites active, and 3 doctrines active. I also finally figure out that to actually unlock anything, you have to hit the tiny little "Info" tab, and that gets you the box to spend the skulls.
The options are pretty cool. At this point I'm actually happy. But that's because I'm patient. I had to figure this all out. There's no intuitive menu structure, explanation, or anything that explains how the system works. You've got this really cool mechanic to customize forces, but it's not apparent how to use it at first.
Consider making the menu system better, a quick "How to" tutorial of a few text boxes, just something to guide users on how to use the thing.