One major downide of atom is that while you can develop your own plugins, core atom modules are extremely slow to accept contributions. I spent a lot of time on something (https://github.com/atom/tree-view/pull/913) which makes sense in core but is hard to do as a package, and it's been ignored, along with 42 other PRs on the same repo.
I really like Atom for its hackability, but an important part of hackability is community contribution. Their roadmap is 404ing (http://blog.atom.io/2014/10/23/public-roadmap.html), they don't really take public contributions, and AFAICT there's no public product direction of any kind. I hope they solve this - Atom is too good to lose to bad community management.