I have played in several sci fi campaigns in my life -- Star Trek, Star Wars, Traveller, Space: 1889, Space Opera, Blue Planet, varioius home made games. As such I can say that the system I prefer is ... it depends.
If I am playing a hard sci fi game, I want a set of rules that reflects that, probably pretty rules-intensive; if I am playing standard science fantasy (aka Star Wars), I want something much lighter and quicker. Heck, Star Wars plays well if you use Fudge or Over The Edge; hard sci fi would be crippled with such rules.
I am still looking for the "best" rules, even for the specific genres...