Haven't had much opportunity to have nails driven into my testicles.

For me, it's the unrenameable, unmoveable, non-hidden snap directory in my home directory's root that doesn't even follow the naming convention of the other directories in there.

What everyone else has already said, plus sudden updates that nuke active applications.

And also the fact that the store backend is proprietary

Mostly start up time for me. It just takes the programs longer to launch.