I have Lion installed on several different computers and it runs well on all of them...now. One of the three upgrades went perfectly well. One not so well. One was a disaster. Interestingly I did the same thing with all three computers: in the Users & Groups control panel I turned off all my login items in case any of them were incompatible. Knowing there could be some incompatible plug-ins and extras, I looked in my Library folder and moved all the contextual menus, system services, input methods, input managers, and PrefPanes. I didn't delete them, I just put them into new folders with the original folder's name plus disabled. For example input methods disabled. Then I used the standard upgrade.
As I said, one upgrade was perfect and I slowly added the items I'd removed, finding a few that were incompatible and throwing those away. One upgrade resulted in a computer that was slow and gave me the beachball a lot and one was a disaster. In the case of the latter two, having recent backups, I erased the hard drive, installed Lion, and used Setup Assistant to restore my data, configuration, and programs. And now I have 3 happy computers.
Why was one of the three perfect and the other two not so much? I don't know. Nor do I know why at work we had dozens of successful installs and just a handful of failures. All I know is that we saw this same kind of thing with Tiger, Leopard & Snow Leopard too - the majority of people who complained about upgrades that didn't go well used Upgade and when they used a different method to reinstall the OS most of them saw their problems go away.