Well there’s been almost half a million downloads of Audacity 2.0 since it was released and we’ve not been flooded with complaints.
Perhaps you missed the step to select associating projects with Audacity during the installation, or perhaps there was a registry error that prevented the file association from being updated correctly. There’s quite a few things that could account for the problem, but given the rarity of the occurrence I don’t think that it looks like a problem with the installer. If it is all working correctly now, that’s the main thing.
What created that registry key (HKEY_CLASSES_ROOTApplicationsaudacity.exeshellopencommand) was setting an association with Audacity for a file type. The above registry key then points to 1.3.14 Beta. That fact means you cannot then set an association to 2.0.0 until you rename the 2.0.0 audacity exe to something other than “audacity.exe”, or edit that registry key to point to the 2.0.0 audacity.exe (as you did).
It is not recommended for most users to directly edit the Windows Registry. You could damage your computer.