When people give you a hard time, Elestan, it is because you say things like “not working under a typical contractor arrangement” as if you know what you’re talking about. There’s nothing unusual in the contract other than it’s pretty draconian on not allowing Paul and Fred to even use the trademarks “in any way”.
That's interesting; so are you saying that most game developers only yield the trademark to their publisher, while retaining the copyright? If so, that's quite different from what I've seen in other parts of the software industry.
Feel free, Elestan, to specifically list what you think they have a copyright to and why Stardock would care about it except for distribution the old games. Some art? Ship designs? A user manual? DOS source code that no one appears to have?
I can tell you what I’d care about: certain specific alien art designs that are fairly unique and the classic ship designs. But that would require knowing who actually owns them and can prove they made them (Which arguably they were derived from other things as Kavik endlessly tries to argue).
I'll assume that this counts as a waiver on your earlier request that I avoid discussing the case here. 
At this point, I need to make a "Not a lawyer" disclaimer, to make it clear that I'm speaking as a layman and not a professional. If anyone relies on what I say to make a legal decision...they're an idiot. I'd also request that any lawyers who might be offended by the mere act of speaking on this topic refrain from derailing the thread with attacks on my already-acknowledged lack of legal qualifications.
With that said, the generic answer is that anything with a creative aspect to it is covered by copyright. That would normally include art, music, fictional setting, characters, dialogue, plot/story, fictional history, etc., to the extent that they expressed creative decisions. But in this case, there seem to be at least three extra twists:
First, the music is special, because it seems like it was probably non-exclusively licensed from third parties like Riku, so P&F would not be able to control it.
Second, some of the other creative elements may have been made by others, without getting a copyright assignment. My assumption is that Paul is getting those assignments, such that most or all of these will eventually get resolved in Paul's favor, unless he's fallen out with or cannot reach some of the people involved. Greg Johnson's earlier posts on this forum certainly indicated support for Paul being the primary origin of the game's creative aspects.
Third, Paul&Fred did not register their copyright within five years. My understanding is that this means that they actually have to prove what they created, instead of it being presumed as stated. My assumption on this is that they will be able to do so; it'll just mean that have to do a lot more work digging through their old notebooks, etc., and end up paying a much higher legal bill.
And yes, Stardock could claim that, for example, that the flying saucer aliens in their games are creatively derived from the generic flying saucer alien trope that's been in SF for ages, and not creatively derived from the specific flying saucer aliens in the UQM universe. Or that its other elements are not similar enough to infringe.
But my understanding is that the similarity question is ultimately a jury decision, which makes it highly unpredictable. If the case actually goes to trial on those issues, my non-lawyer opinion is that it's probably going to be a crapshoot (and I've heard the same opinion from actual IP lawyers).
But even then, how much is that worth? Compare that to the confusion in the marketplace and illwill they caused with their actions prior to any legal filings?
It seems to me that calculating damages here is also in the realm of guesswork. SC:O hadn't even been released yet, so there's no telling whether it would have been another GalCiv or another Elemental, nor can we say with any certainty to what extent P&F's post changed things. We also can't distinguish harm caused by P&F's post from harm caused by Stardock's own litigation choices.
My own opinion is that if you compare this reality to the alternate reality where P&F avoided using the phrase "Star Control" in their post, there aren't going to be many differences outside of the lawsuit itself. The media and fans for whom "Star Control" meant anything would all have connected P&F to the original games anyway, whether they referred to them as "Star Control" or "The Ur-Quan Masters".
By contrast, if you think your competitor can represent their new product as a sequel to your product, why have trademarks? Why not just claim your product is the sequel to Minecraft or Halo and get a bunch media coverage and confuse people into thinking there’s two new Halo games or Minecraft games coming out.
I don't think these examples are very applicable; since Minecraft is a builder and Halo is a shooter, they have minimal literary elements. A better example would be "Betrayal at Krondor", where the story was created and copyrighted by Raymond Feist, and the game took place in his fictional world, but was developed and trademarked by Sierra (which was eventually bought by Activision). I'll grant that SC2 was less literary than BatK, but certainly moreso than Minecraft or Halo.
Semantically, "sequel" could legitimately be used to denote either a literary successor or a successor product. But I don't claim to know enough to resolve the legalities of its use in the context of a copyrighted creative work that is also a trademarked product, with the trademark and copyright ownership separated. Who has the right to use the word "sequel" in such a situation? You've previously said that you have case law on this topic, and I'd love to see it.
