The notification popups are sort of awful, yeah. The concept isn't necessarily terrible, but the usage in practice is annoying. Like how Pidgin by default pops up (or used to pop up) a notification for every message, even if the actual message window is open and focused. I think it's fine for stuff like volume changes or network connectivity changes, though.
Realistically, though, it's hard to make *more* of a UI trainwreck than a typical application does (open-source or not). Usability studies are no guarantee of anything, but they're a step in the right direction. I remain optimistic.