It would be great if you could put neat holes into vertical terrain without it stretching all the way to the top and bottom of the face.
It would also be great if you could designate structures to flood fill or not if placed underwater. Or failing that, if it's too tricky to pull off, how about some purpose built structures intended to be placed underwater with airlocks, or some such, that allowed you to enter and not be swimming any more.
It would be nice if when you pulled up the weapon wheel it also indicated what gear you've got. I've lost count of the times I've been up high somewhere and couldn't remember if I'd been given a wingsuit or parachute or not.
I'm sure I'll think of a few more as time goes on.