Most importantly I miss SFTP. There's already a github project for sftp, but at the moment it's almost unusable. https://github.com/jules-r/atom-sftp

I also really miss bracket highlighter, it's a super small tool, but very useful. You could tackle the bracket highlighter plugin, it might even be possible with pure less/css depending on if Atom already has this built-in.

And I miss being able to run a Python REPL in Atom. Python and JS are my main programming languages.