I use Ubuntu as my workstation OS, and manage quite a few Ubuntu cloud instances ( among others ). There are so many small issues we have to deal with everyday. On the desktop side there minor "polish" issues, like settings that reset on reset ( e.g. Bluetooth radio ). There are random lockups ( I've tried several common systems, including one that came with Ubuntu). I have a brand new Dell XPS 15 coming in a week I hope fairs better.
The fact that there is no way to use hibernate. It's 2015 and we can't use hibernate! A basic OS feature.
On the server side, upstart is an absolute nightmare.
Ubuntu launches on every device that gains traction ( Ubuntu for tablets, phones, etc ). But it seems the basic OS is still very rough around basic edges. But I wish they would just give us a polished desktop. Even if it may cost more than Windows I'd personally pay for it.