Yes, that's the final mission ... for now.  You can currently fly around and continue to explore, explore planets you didn't before, etc.  The other alien races have some comments on what you accomplished, so you might want to visit them again.

As for future missions, see this thread:

https://forums.starcontrol.com/491316/page/1/

There are already a couple of Stardock supplied mods available that add a mercenary hunting mission and a galactic zoo, and note that in the original post of that thread Brad says that they will continue to add to the base game.