"The Ur-Quan Masters" was always meant as a subtitle.  It sounds like a subtitle - it doesn't give any hint at what's behind the game.  Sure it works for name recognition, and I suggest keeping it for that reason.  But I would strongly suggest moving it back to that status and creating a new overtitle name.  The community is large enough that a new "franchise" name won't hurt recognition.  GalictiQuest (GQ makes a cool set of initials) perhaps.  "GalactiQuest: The Ur-Quan Masters".  Sounds catchy in a 1980's sort of way.

Sequels, prequels, anything you like can be made with numbers.  GQ 2, GQ 0 for a prequel (or -1 if you like).  Don't have to worry about whether or not the Ur-Quan are in the game or not.

Of course "GalactiQuest" is just my own toss-out after a half second's thought.  Use ir or not, whatever, the main point is to come up with an overall franchise name that's new and unique.  This community has accomplished a lot on its own.  No need to be tied down with other people's names any more.  Come up with your own - you deserve recognition in your own right, not just as game cloners.