For really, and I mean really cleaning all remnants of previous versions, manual labor is the only way to go. Do not forget cleaning up the registry as well from RegEdit.
During the development cycle to prevent intra-version (build) conflicts, we create and maintian 'clean' OS images in a pre-CSn state. If you don't have the luxury of such an image then, then you will have to rely on uninstall + clean-script, but as you discovered that does not really rid you of EVERYTHING, especially on windows.
The good news is that I have never experienced usability problems or non-valid bugs which were caused by having two release versions of the same product one one OS> In fact, I run at least one system all the time with two or more consecutive versions on it for the sole purpose of comparing behavior between the two, and have never had it lead to problems. So I'm certain you will be fine with justy uninstalling and manually migrating your old project directories as needed. And running a legitimate clean script afer that will be more than enough. But if the mere idea of anything CS-Previous bothers you, then you will have to go into the registry and the various library and some 'hidden' directories and dlete everything by hand. But I DO NOT recommand doing that because if you don't really know what you're deleting in there, it could easily cause much more serious problems (like making your current version unusable) than it would solve.
Personally, I'll be doing a complete wipe and reinstall from Windows on up. I figure installing CS6 is a good time to do that, as it hasn't been done in over a year and, well...junk accumulates.
Indeed, if you have a clean image to restore to or don't mind re-installing the OS from scratch, that's a good thing to do, if only for the sake of your OS. But as for PrPro, there's not a whole lot of cumulative files other than project files (which you'll probably want to keep anyways) and preview files which can easily be deleted per project from within the app or from the OS at the default project location or wherever you've pointed your projects to. Of course, if you're in the habit of saving your projects all over the place, it may be hard to track down all the associated preview files, which would be a good reason for an OS restore.
In summary: If you don't have any reason to keep CS 5.5 around (like for comparison tests or opening legacy projects natively), then it's best to remove it to save yourself some confusion and a lot of space. Running the uninstaller and a valid cleanscript <http://www.adobe.com/support/contact/cscleanertool.html> will suffice for that. But if you like to be sure that ALL previous CS remnants are gone, then restoring or re-installing or the OS is the only 100% method.
OP: Do you feel that your question has been satisfactorily answered?