I actually do run ion3. The only problem I've had so far is that some of the Alt+ keyboard shortcuts interfere with some Emacs shortcuts. One off the top of my head: Alt+G.
I just remap/unmap the ion shortcuts to get out of the way of emacs. I have a friend who swears by setting ion's Mod1 to capslock, but my pinky just can't handle that.
Set Ion's mod key to super (aka the windows key) and everything starts playing nicely :p