Mostly small things like "stickiness" when moving mouse between monitors, or the conflation of apps & windows on the launcher bar that always seemed to make it hard to switch between different windows in the same app, or launch new windows of the same app. My memory is a little vague though since I tried it briefly when I got it at work a few years back, didn't like it, and switched to Cinnamon which I've been using since. To be fair to Canonical, that switch was painless and Cinnamon hasn't been without it's little idiosyncrasies as well.

My guess is that people think Canonical should have been focusing more on general distro reliability (e.g. the infamous "/boot fills up with kernels" bug) than reinventing parts of it. Hindsight is 20/20 though, we'd be having a different conversation if Mir had proven a big step forward over X.