I agree. I use the command line for everything but staging, and I often only stage parts of files while discarding a few leftover pieces I forgot about. I use sourcetree, but the concept is the same. GUI git is really nice for staging parts of changes. And then I usually commit via the GUI too, since I'm in there anyways.
But then I figured out that Atom's git integration is actually quite neat and I started using it mostly to do `git add -i` as it makes staging files or parts of files really easy.
I still don't trust it with pushing/pulling, switching branches etc. so I still drop to the command line for those, but the atom git integration is incredibly useful for seeing your changes and committing a particular part of them.