Stardock's position is that Paul and Fred own the copyright for the lore and aliens of the Ur-Quan conflict lore.
Stardock owns the publishing rights for Star Control 1, 2 and 3 and the lore of Star Control 3.
The Ur-Quan conflict and the Crux conflict each exist in their own universe within the Star Control multiverse.
Star Control has never been about a single set of lore. The original name for Star Control was going to be "Tales of the Ur-Quan conflict".
Of the three Star Control games, only Star Control 2 touched on the Ur-Quan history.
For me, Star Control is about Earthlings going out and meeting aliens, exploring worlds and delving into an epic story.
As a practical matter, the Ur-Quan lore isn't relevant as even if Paul and Fred were fine with us using their lore, we couldn't really use it anyway. We can't redo Star Control 2. That already exists as the Ur-Quan masters. And there is no scenario where we could continue the Ur-Quan storyline 25 years later from a marketability point of view.
When I first heard there would be another Star Control game, I flipped out. However, after seeing what this new game will and won't be about, my heart sank. I cannot tell you just how much this means to me.
First, you absolutely must separate the lore of SC 1&2 from SC 3. Star Control 2 was one of the greatest games ever created, the storyline of which has greatly influenced my writing, storytelling and gaming. The idea of a massive conflict centered on taking down such a formidable opponent (Ur-Quan), only to discover that this opponent was actually protecting you from an even GREATER threat (Kohr-Ah), was so masterfully executed and has stuck in my mind ever since. Often when films or games involve a plot like this, it comes across as cheesy or as a need to simply "outdo" the previous plot. "How can they top this?" people ask.
Star Control 3, which was not created by the same people, was an absolute disaster and a complete letdown to fans who were enamored by the rich storyline created from the first two. The Star Control that we've been waiting all these years for was a new sequel to Star Control 2 that completely ignored everything from SC3.
Your plan to make the next game a prequel, or an origins story, is brilliant. As you say, from a marketability standpoint, the game must reintroduce the franchise to a public that has either forgotten, or were simply not alive yet when the original games were released.
However, moving forward with a Star Control game that is actually related BY NAME ONLY, makes no sense whatsoever, and I would argue is the complete opposite of what you should do from a "marketability" point of view. Sure, you may get new players who've never heard of Star Control (for which the name would actually mean nothing at all), and you may get a few players who remember Star Control and buy it out of curiosity, but for the many older fans of the original, this will be a complete disaster. The fans who know it shares nothing in common with the original may opt NOT to buy the game at all, or worse, you will have hardcore fans who eagerly buy the game, but who then leave scathingly bad reviews upon their discovery that NONE of the original aliens appear in the game, potentially turning away even new players based on the reviews.
The only marketable strategy would be to do your utmost to acquire the rights to the lore of the originals by either purchasing them completely (though unlikely because Ford and Reiche have resisted this in the past), or by leasing them on a per-game basis through some negotiations with Ford and Reiche. Or by simply NOT calling it Star Control.
To put it another way, would you enjoy a "Star Trek" game or film, which did NOT include ANY of the aliens or lore of Star Trek? Simply calling a film "Star Trek" does not make it Star Trek. The same is true for "Star Control."
For this game, in its current form with no relation whatsoever to the originals, I would pay nothing for the game. For a true Star Control game that honors the lore of the original and includes a Ford/Reiche stamp of approval, I would pay more than $200... right now, up front.
Do or do not. There is no try.