Well, that's easy to say but it may be a little simplistic when upgrading from Vista, though I would definitely agree that a fresh installation is the way to go if starting from Windows XP.
When I built the machine which now hosts W7 I did a fresh Vista installation and rebuilt my software environment. That took over a week to complete and, being retired, I'm not just talking about the odd hour or two every evening. I've done both OS upgrades and fresh installations going right back to Windows 2 (yes, I actually used it) and both approaches have pros and cons.
The glitch with "User" data appears to be the only one that might have caused grief and it may have been down to the fact that when I installed Vista, the precursor OS, I initially created the main admin account with the name "Bob Andersson". For reasons I needn't go into, fairly late in the day I renamed that account as "Bob". That worked fine, as it should as Windows specifically provides the option to rename, but the file names hanging off the User folder don't
change. I'll have to do some more research but I think it's more than possible that the W7 upgrade installer got confused by this when handling the \AppData subfolders as all the other "User" data, such as the Desktop and much else, did get reinstated correctly
So, with that one caveat, I'd have to say that the upgrade went well, so far...