Actually I desire with all heart to see a new FS3, primarily because I always wanted to see a canon ending (if not, what the purpose of Shivanity is) but I see that it would probably kill a great deal of FreeSpace fan creativity, all those crazy-mind-maded Shivan theories be shunned aside, and the excitement to forge ridicolous (but creative) or dramatic ideas for an ending to the FreeSpace saga.
So I'm quite divided. Of course, it'd be nice to see that we still retain our creativity as the creators of a fan-conceptualized FS3, yet still there would be a canonical ending for the FreeSpace series (or perhaps only a continuing) and an explanation for the Shivans' existence.