I agree that it's kind of annoying at first that there is no crouch/cover toggle in singleplayer, but I was able to do it even with the alternate 2 controller configuration. Not only that, I use ironsights a lot, maybe I'm just used to using the shoulder buttons from flying in Warhawk.
Since multiplayer has no cover system, there is a crouch toggle there. We'll have to get used to not having it for singleplayer.