The Gemini rules for Warhammer 40,000 are essentially a set of house rules for Games Workshop’s flagship product.
I think that the author is correct in his premise — that the Rogue Trader rules were perhaps the best.
Rules: Science Fiction
Our Space Age Army Rules
Our Space Age Army is a set of solo, science fiction platoon level rules. Lots of other stuff at the main page here.
GrimDark Racing One Page Rules
GrimDark Racing is a set of simple rules for races in the Warhammer 40K universe. Just use models you already have. There’s plenty of violence, of course.
Slammer Skirmish Science Fiction Rules
Slammer Skirmish is a set of free wargames rules for science fiction skirmishes. The author writes:
Slammer is a set of wargame rules for Science Fiction skirmish games using miniatures. Slammer is not tied to any specific background or company product line, you can use whatever figures or models you have. I intended from the start that Slammer would be flexible and adaptable to different scenarios. I have intentionally kept it fairly ‘loose’, particularly in areas like troop motivation and Hollywood heroics. Slammer is meant to be fun!
Railgun: 2000 Science Fiction Rules
Railgun 2000 is a set of free wargames rules for science fiction armored combat. You need the Fistful of TOWs rules to play.