One reason I like using Emacs is that I can run it in a terminal - e.g. over ssh. I am skeptical I'll be able to do that with Atom (without using X forwarding).
On top of that I can be up and running with Emacs on a fresh install of just about any linux distro: install via the distro's package manager, drop in my configs, done.
The big difference from my perspective is that Atom isn't currently FOSS. Other than that, the maturity of the emacs ecosystem is both one of its greatest features and a bit of a curse.
The non-FOSS part is the part that bothers me the most. Maybe bothers is too strong a word. It's just hard for me to get into a text editor without knowing that the community could pick it up and run with it, if the originator dropped it.
Not sure if that's an unfounded fear, but I don't want to invest time customizing a platform and writing plugins when it could close shop in a second. I suppose I could say that about a lot of things I do customize, but it's hard when the FOSS text editor world is so rich.
40 years of legacy decisions can be a huge weight on a project, but reinventing a newer, rounder wheel has pitfalls as well. I'd love to say 'I want a modern version of emacs' (or, in my case, vim), but I'd be terrified that I'd end up with a TextMate2-style second system syndrome.
It looks like the GH guys have worked around this problem quite well, and I'm looking forward to begging, borrowing, and then just begging again if I get a chance to try it out.