When you create a new buffer and hit save, Atom will present me with a save dialog and the default selected folder is the project root. That’s almost never the place I want to put a file.
Sublime Text was a lot smarter with this — although I do not remember the exact heuristics. For example, it would propose saving the file in the same location where the file you last had opened was. This worked really well for me: Usually I create a new file by splitting an existing file, creating a test for a module (and those two are in directly adjacent directories) or similar.
Even if I want to save to the root directory, which is the current behavior, navigating upwards in the file save dialog is really simple.
PS: I am using Atom 0.187.0