The limitations feel very few, and as someone who spent a LOT of time getting my Vim environment exactly as I wanted it, switching over to Atom was a breeze as I went through my .vimrc trying to match functionality; most of it was already there.
One thing I wish they would implement (and I'm sure it will come with time) is the ability to fully navigate the file tree with the keyboard, similar to NERDTree. All you can do right now is arrow up and down, after toggling over.
I've heard its like Emacs -- and now I know what people are talking about!