I upgraded to Ubuntu 13.04 a while ago, and were curious to see how well FS-UAE runs on the current version of Unity (the default desktop in Ubuntu). Unfortunately, it does not run that well by default (same as 12.10).
The problem is really only in windowed mode. FS-UAE syncs to vblank by default, and in combination with the Unity compositing / indirect rendering, the performance is bad, with laggy / choppy rendering (1). When using video_sync = off, the performance is “normal”. On the bright side, full-screen performance seems to be improved when syncing to vblank.
Let’s hope Ubuntu / Canonical manage to fix the OpenGL support with Mir (though I would rather see them joining forces with Wayland). For the time being, I’m using the MATE desktop on Ubuntu. Without any compositing / desktop effects, OpenGL performance is nice, and FS-UAE frame rates are as smooth as can be (2) 🙂
(1) With official closed-source Nvidia drivers.
(2) With monitor running @50Hz of course.
FS-UAE for Ubuntu 13.04 is available from a PPA.