I honestly don't see how this is a problem with the windows upgrade. honestly, i worked front-line support for vista when it came out, and we saw a lot of the same thing. in my mind, and I do not work for microsoft, and these are my own views, and not those of MS, but the problem is, people are expecting to much of the upgrade install, a good chunk of it in my mind is a best effort attempt to try to carry things over. but there are so many factors that can't be accounted for.
When I was on the phones working with this issues, there was a lot of routine prep work that I did prior to running the upgrade. like removal just about any program that had some form of built in registration because those registrations did not always carry over, and often times were impossible to re-register after the upgrade. removing any 3rd party drivers, because obviously a driver made for XP did not always work with vista, or perhaps caused file conflicts with the vista driver. MS software other than windows was also removed, reason being, things like .net framework were part of vista, and did not need to be ported through an upgrade, you can see how this may cause problems. Antivirus and Spyware removal software, often can try to undo changes being made during the install however. and the list goes on. Its not that all of those will break the install, but some may conflict after the install. . . The upgrade is really meant to be installed over a clean installation of the original OS, any thing more in my mind, is best effort
I once had a user called in after an upgrade with a startup error about the vista ui not working, although everything seemed to work fine, it turned out the customer had a vista theme pack installed on XP that wasn't removed prior to the upgrade. also performing a clean startup procedure helps, I forget which KB article that is detialed in, its been so long.
another thing i saw on several occasion were corrupted registry permissions carried over from the old OS. they not have caused any obvious problems before, but after they upgrade could cause problems trying to uninstall or update programs after the upgrade
Sometimes prep work like this for an upgrade can take as long as just doing a clean install to begin with. and it may not always be as bad as i might be making it sound either, a lot of the time it works without doing any of these steps. All I'm really saying is, I think some people are expecting to much from the upgrade installation is all