In just about every XCom-like game I've played, when you create a new base, it has a preset default layout. A terrible preset default layout with alien accessible hangars scattered all over the place, connected to everything else without chokepoints. If you want to specify a layout for defensive or aesthetic purposes, you're forced to destroy and rebuild rooms, which seems silly if you just built the base.
It'd be nice if we had the option to define our own base layouts right off the bat. (Just give us the default rooms with no cost or building time.)
Also, it would be nice if we could specify connections between facilities within the base, rather than having them automatically connect to all adjacent rooms. All rooms would still have to be connected, of course.