Most other rights given in the original 1988 contract terminated if they stopped receiving at least $1000/year in royalties, which happened around 2000.
And no, it wasn't most other rights. It was specifically just the characters and settings from SC1/2 (which Fred acknowledged and which Stardock is not disputing). Yes, Paul and Fred own the rigfhts to SC1/2 aliens and settings. However Stardock have a perpetual license to USE them if they want to (which they have declined to do).
Again, I am not a lawyer.
First of all, not a lawyer either. There has never been a time when they did not own the IP of SC1/2 - it didn't revert to them because they always had it. It is true that Accolade was given an exclusive license, but the case that it's expired seems pretty strong.
2.2 of the 1988 contract says that if the developers stop receiving $1000/year in royalties, Accolade loses its right to sell or license their products. Reiche and Ford say that happened around 2000 - I doubt Stardock has somehow found Accolade/Infogrames/Atari accounting records proving otherwise. So what about making new content? The 1998 addendum gave Accolade the license to make sequels with their IP, but had a three-year reversion clause giving those rights to Reiche if nothing was made. So if those expired, that just leaves the trademark and portions of SC3.
Also according to their complaint, Atari agreed that the license to distribute Star Control had expired. We haven't seen the e-mails but I don't think it would be in a legal document if they couldn't back it up.
Furthermore, 7.1 of the contract says that if the publisher goes bankrupt for at least 90 days, "all rights to work or derivative work shall revert to developer." I don't think Accolade's merger with Infogrames involved bankruptcy...but even if the license hadn't already expired on other grounds, it certainly seems to apply to Atari.