"...but in the latest version it also does not install them as a separate application that can be uninstall individually from the app itself"

Actually, is it possible you're looking in the wrong place for the uninstaller? I also did not find it at first, because I was looking for something like "Skype Click to Call" in the uninstall programs list... Actually, it's listed as "Click to Call with Skype" (so it's under "C" in the alphabetical list, not "S"). I think this is slightly different from the old Skype toolbar, but hopefully what you're looking for, since it is indeed automatically installed with the Skype 5.5 update.

I wonder if Skype has any good reason for causing confusion by having a different add-on removal process than what is typical for the huge majority of other Firefox Add-ons. My guess is that because it's not installed from within Firefox, it also can't be uninstalled that way.

I did not experience the error you did, but I did experience the annoying / unscrupulous behavior of installing an add-on during a Skype update without asking me if I wanted the add-on first (or at least the option was not obvious) -- especially bad considering the major performance and stability problems caused in web browsers by past versions of Skype add-ons/toolbars.

That's great if Skype thinks their new add-on version is now rock-solid, but their self-confidence is not a reason to modify my web browser, which is a critical tool in my daily business activities... leave that decision tied to my confidence in whether they deserve another chance or not, thank you!

Go to Tools- Adds-on, on the Skype section click the disable button good luck