Stardock has had an interest in Star Control (and Master of Orion) for a very long time. In fact, this Gamasutra article from 2008 shows CEO Brad Wardell pitched this to Atari years ago, but as we know, nothing came to fruition then.
Fast forward to just yesterday, as Wardell announces post Atari asset auction that they have succesfully acquired the rights to Star Control, and are now planning a reboot of the entire franchise. In fact, his description of an XCOM styled reboot inspired by the 2nd game falls in line with his thoughts in the Gamasutra piece, explicitly stating he has no intention of acknowledging SC3.
Star Control was originally developed by Skylanders creators Toys for Bob. Paul Reiche III and Fred Ford made Star Control 1 and 2 for Accolade for various systems, and balked at making Star Control 3 with SC2's budget. Eventually, Accolade itself would go out of business and sell its assets to Infogrames in 1999. Infogrames itself would later buy and rebrand itself under the trademark Atari, Inc.
Reiche and Ford retained their copyright for the first two Star Control games, although they didn't own the name itself. They decided to release the source code for the 3DO version of SC2, as well as a port of the game to modern consoles under a Creative Commons license, renamed The Ur-Quan Masters. This version of the game boasts online multiplayer melee, and has been ported to Windows, Mac, Linux, Wii and even BSD.
Answering questions on the Ur-Quan Masters forum Reiche explains that they have yet to receive word from Stardock about the planned Star Control reboot. He believes that Stardock was able to acquire all copyrightable content related to Stardock not connected to the 1st 2 games. Reiche concludes that Toys For Bob never sought the Star Control trademark themselves because they did not see any opportunities to use it immediately.
Toys For Bob is doing just fine with Skylanders, but everyone's eyes are on Stardock now and what they will pull off with this reboot.
