Every GS/Sniper knows how clunky and buggy cover is currently.
My proposed fix is this:
If an ability that requires cover is used when the character is not in cover, the player is instantly dropped into cover and the ability activates.
This eliminates so much of the clunkiness that these ACs experience with trying to get into cover.
Are you using "Take Cover" or "Crouch?" I originally used Take Cover, but i use Crouch now and it has removed all the issues you described. I drop instantly into cover and use my moves.