Avoid RIFTS for rules- the rules are the worst part of the game. Use RIFTS for its campaign setting.
For a good "hard" sci-fi game, its difficult to find one better than Traveller. It is, in almost every sense of the word, the D&D of Sci-Fi RPGs. It is also available in a multitude of systems, including D20 and GURPS.
That said, Alternity/StarDrive, an OOP TSR game comes close to it in quality. As I recall, it's kind of a missing link in RPGs- its still a lot like 2Ed D&D, but it has elements that would later appear in D20.
Prime Directive is a game designed around Classic Star Trek, and is in print in several systems (original, D6, D20, etc).
HERO has a sci-fi setting called StarHero. Personally, HERO is my favorite system, but its crunchiness can be a deterrent.
Mutants & Masterminds, because it is a good superhero game (second only to HERO, IMHO), could be used to run almost any genre of RP. I see it as kind of a rules light amalgam of HERO and D20.
The current version of Paranoia, while seemingly an odd choice, actually works well for what you're planning. The current edition provides rules for running the game as it has been traditionally played for so long, but also as a serious sci-fi RPG. Sub a large starship for the Alpha Complex, and Cylons for Commies, and you're good to go!
There is an old SPI game, long out of print, called Universe. It was nearly as good as Traveller, but it was released without support- as I recall, SPI folded shortly thereafter.
There is a new game by the same name- I have no idea if its related in any way- but it, too, looks to be a good hard sci-fi game.
A new entrant I'm looking forward to buying is Terran Trade Authority, based on the classic future history series by Stewart Cowley. The first book by Crowley, Spacecraft 2000 to 2100 AD, is the only one I own, but the art and storylines simply ROCK! Check it out at
http://www.terrantradeauthority.com/