The legal status of pretty much everything related to Star Control is in dispute right now. Here's how I understand it:

The duo that lead the development of the first two games, Fred Ford and Paul Reiche III, are on one side. They claim that they licensed some rights, such as the "Star Control" trademark, to Accolade a long time ago. Atari bought Accolade years later, and then Atari went bankrupt. Meanwhile, FF and PR3 were working on other projects and didn't have the resources to make another Star Control game. Accolade made a game called Star Control 3 without any/much involvement from FF and PR3. It's not considered canon.

When Atari went bankrupt, the company's IP was sold in an auction. Stardock bought the "Star Control" trademark and basically all the rights to Star Control 3. They started developing a game called Star Control: Origins without the involvement of FF and PR3. They did consult with them about the IP, but apparently no formal agreements were made. Stardock announced that it wouldn't be using the lore from SC1 or SC2, to leave room for FF and PR3 to create a sequel later if they wished.

After the success of Skylanders, which their company created, FF and PR3 recently announced that they had the time and the resources to work on "a true sequel to Star Control 2". Stardock filed suit against them for using the "Star Control" trademark, which they believe they own. FF and PR3 filed a counter-suit, claiming that Atari's license to the Star Control trademark had expired before the auction took place (or as a result of declaring bankruptcy), so it wasn't theirs to sell to Stardock.

Basically, we're just going to have to wait and see how it all turns out. Meanwhile, you can play The Ur-Quan Masters, which is an open-source version of Star Control 2, but without the "Star Control" name.