Yes, unfortunately the git upgrader withe 2.0.0-alpha6 was broken, so it won't update itself properly. You'll need to delete the Packages/Package Control/ folder and then follow the instructions on https://sublime.wbond.net/installation
to get it to go through properly. I guess it lived up to its name of being an alpha.
In the new version of Package Control, only packages that are listed as compatible with your version of Sublime Text will show. Thus there are quite a number of ST2 only packages that won't show up in ST3. There are also a few ST3-only packages. https://sublime.wbond.net/stats
has the details.