Yeah, direct control would be cool, but we had no time to implement it.
Intelligence is just an alternative mechanic for building reveal. Yet again had no time to make it interesting, so it's just chances to reveal a building/intercept enemy spy.
Had no time for a tutorial, sadly. DEFCON stages intentionally have no visible timer (with the logic that you can't predict it irl, I guess and that make the game a bit more stressful at least in theory)