Wow. A good question.
Assumptions: Alternity system is not heroic but realistic game. Dark*Matter and Star*Drive still used as settings under Alternity.
Keep: MOGA roll results, durability tracks, weapons and armor, F/X and mindwalker skills, miin/max limits on ability scores based on species,
Modify: Rank benefits as Perks (feats) with requirements, simplify XP, simplify skill cost charts,
Remove: Professions, the forcing of skills under an ability score (so maybe ability scores do need to be revisited),
The big thing that I have to remember is that Alternity is NOT a heroic game. I tried to use it for a fantasy game and I like heroic fantasy. So, Alternity did not work as much as I wanted it to work. It's great for modern or SciFi in that regard but not heroic fantasy. Having said that, if it was in print again, I would love to see an options book to have ideas for heroic games, different magic systems, etc.
After that, I would like to see things simplified. The variable skill costs merely added in complexity to the character creation rules without adding any value to the process. If there is to be a gamemaster's book and player's handbook, I don't want to see the symmetry they were doing for a while, where a chapter in the PH and GMG are on the same topic. They need their own topics.
I really liked Alternity and used for Dark*Matter or Star*Drive, it's a great system. What wore me down and stopped me using it was that it wasn't in print. After ten quick campaigns of it, over ten years, I had "played it out" such that it was boring to me. OOP came to mean no new options and stagnation. So, for me, that's why I don't mind new editions or extra books for a game, as more options are good!
Good question! Thanks!