I'm annoyed by the lack of an actual "Home" category in Settings. I like to switch between Google Now and Nova on my N6, and I'm used to being able to set one of them as a default launcher in the Home setting in MM but still maintaining the option to pick the other launcher later. With that gone, you're left with having to choose between "Just Once" or "Always" every stinkin' time you hit the Home button. And if you do pick "Always," you have to install a new launcher in order to get access to whichever launcher you didn't pick.
I tried to set Nova as my default launcher and completely lost access to Google Now. When I tried to open the GN app in my app drawer, I got a useless error message telling me that I had to change my preferences in Settings, but tapping on the link to Settings in that message only made the error message disappear.
A minor point for most people probably, but it seems odd that Google wouldn't do more to keep their stock launcher always available.