I still use Sublime mostly. However, Atom seems to have a thriving ecosystem around it. There are a lot of high quality Atom packages. I believe it's mostly because Atom has a more accessible developer interface for newcomers, being it is just a web app. And it's open source.
Also, Sublime seems to be abandoned for a while. Not that it stopped working or anything.. But I believe the lack of development will push people away eventually.
I just find it funny that replacing "Atom" with "Emacs" in your argument doesn't feel out of place at all.
Well, Emacs Lisp might be less newcomer friendly and it's not a webapp. But still, thriving ecosystem - check, accessible to developers - check, huge number of packages - check, runs everywhere - check.
The thing Atom has which Emacs doesn't is that it's approachable even if you don't appreciate all the customization and the rich ecosystem. You can sit down with Atom and just explore it like you would any other GUI text editor, and it pretty much behaves exactly like you'd expect without having to learn any obscure commands or shortcuts. You can learn the commands and shortcuts (and explore the ecosystem) as you settle in.
I'm primarily a vim user and I still prefer vim to Atom, but within a day or two of seriously trying out Atom, I was probably up to speed with 90% of the core functionality I use in vim on a day to day basis. That last 10% is a bit of a killer, though. :)
How often do most developers set up a new environment? For me, it's nowhere near enough for me to care at all whether my main development tool "works out of the box."
Not nagged to buy within an hour of installation, I'd consider that a plus in favor of Atom.
Of course, Atom is open source and has potentially huge community backing to push it forward (vs. pleas for features and fixes to the other editor's seemingly absent overlord).
tl;dr At this point: not much. That might change soon, though.
When I switched laptops recently, I made the conscious decision to only install Atom to see how things went...so far so good, although at times it does bog down pretty noticeably, and this is by far my biggest complaint. There's also no alt-drag support (to create a straight line of cursors like Sublime), but that's a fairly small gripe.
I loved the plugin ecosystem for Sublime, and in the short time Atom's been around, the ecosystem has already exploded. Lots of awesome themes and plugins are already available, with more coming every day. The low barrier to entry (most things can be done with JS / CSS) probably has a lot to do with that.
I switched mainly because ST2 was acting up, throwing errors left and right. Considered upgrading to ST3, but there were plenty people discussing bugs in that too, and some plugins I use were not yet compatible. A colleague had invites to spare for Atom beta. Checked it out, found it to be 'just like ST2, just without the crashing part' and stuck with it.
Also, Sublime seems to be abandoned for a while. Not that it stopped working or anything.. But I believe the lack of development will push people away eventually.