The installation, update, and packaging story of VS Code is so much more polished on Windows than it is with Atom. I gave Atom a shot for a few months (my employer has products based on it), but it had a tendency to overwrite my settings or completely blow away the .atom folder randomly on updates. And the performance on large files is pretty abysmal (granted Firefox has the same issue opening big plain-text logs, so it's not something that only Atom gets wrong), VS Code does much better.
And if you want to embed Atom within an application, it's great that they've finally updated to make apm use npm 3 so the path lengths don't exceed 260 characters. That's a dumb Windows limitation, but until Microsoft fixes it and enterprises actually update to the version with the fix then it's a fact of life. But atom internally still uses the old nested layout for the built-in modules, so you can't install "portable" atom in a top-level path longer than a few dozen characters.
