Upgraded one machine from Snow Leopard (10.6) and another from Lion (10.7). No issues what so ever. Both still work perfectly, all my stuff from HomeBrew transferred over without any issues either (which is fantastic, did not want to have to recompile all of that stuff).
The upgrade was fast and easy, definitely not something I expected and I had backed up my machine to do an install from scratch, but not required at all.
Did you lose the XCode Command Line tools? I had to install them last week (after I had upgraded) and I swear on my life I had them before. (I would have had to have to have used brew and built as many of my projects as I had).
Recommended by who? The mac pundits that I listen to, Gruber, Siracusa, certainly don't seem to have a problem with upgrading in place on OS X.
And, "no matter which OS" is definitely incorrect. I've done an in-place upgrade of an OpenBSD system for the better part of six years (twelve upgrades, twice a year). The _recommended_ approach on that platform is to do _in place_ - not clean install. It's how you maintain library compatibility with all your legacy apps.
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).
What makes you say that? I've been running the same install since 10.3. It's changed machine several times, and I have run every version of OS X along the way, all without any problems.
