I agree, in it's current sate the cover system is kinda optional. I don't feel any benefits for using it, because if there are just a few enemies you don't really need it, if they are in large numbers the cover melts away rather fast.
As far as the dreadnought its problems come down to clipping. when it hits a pillar or wall it needs to back up and try again instead of just ramming through it an clipping through a non destroyed object.
Also like the idea of a vault system, but will rely on thin cover I guess. But a nice feature in terms of aesthetics.