For me, it’s the linter packages. They just don’t work right. At all. (Also, copy-pasting screws up indentation, and yes, I disabled the “indent on paste” setting, and it didn’t fix anything.)
I gave Atom a good long try, but today I hit my limit when the Rubocop linter kept complaining about a problem in a different file from the one I was in. And I went to the other file and fixed it, and Rubocop kept complaining anyway, and blocking my view of the code I was working on.
You could argue this isn’t Atom’s fault. To that, I reply that I don’t care whose fault it is, I care that it’s stopping me from writing code. If the Atom ecosystem doesn’t have a good Rubocop linter, then I will decamp for an ecosystem that does.
Hello, SublimeText, my old friend. It’s good to talk with you again.