I've had no more problems with the Lion machine I upgraded to Mountain Lion than I have with the two machines I did clean (USB stick, NetInstall) installs on, and the same was true when I moved from Snow Leopard to Lion.
With that said, there are fewer things that can automatically go wrong in any clean install (as opposed to the things that can go wrong manually with a clean install, like forgetting to deactivate Adobe CS, or that scripts accustomed to sshing in to your server don't take kindly to unannounced host key changes).
With that said, there are fewer things that can automatically go wrong in any clean install (as opposed to the things that can go wrong manually with a clean install, like forgetting to deactivate Adobe CS, or that scripts accustomed to sshing in to your server don't take kindly to unannounced host key changes).