Well, I've gotten and read my copy of Starsiege: Event Horizon. For the most part I like it. The "trappings" system that allows you to build tech, weapons, aliens, ships, planets, psionic powers, etc. is a little too picky (not the work I'm looking for but it's the best I can come up with right now). The size score is particularly problematic for my OCD with each increase in "size" doubling the previous size - so a human is "size 10", a "size 9" alien is 3 feet tall, and a "size 11" alien is 12 feet tall. Weight is also an aspect of size so an alien race that averages 4.5 feet is either a thin/light size 9 or a thick/heavy size 10. Apparently there are no aliens of human proportions that stand 4.5 feet tall.
suggested HC SVNT Dracones but I've not been able to find any solid info on the mechanics and I'm not in a financial situation where I can buy a game blind so I can't say yet if I like it or not. It does look interesting from what I've seen but I'm not sure it's what I'm looking for.
suggested Stars Without number and Machinations of the Space Princess - both of them OSR games. I'm a big fan of old-school games and old-school revivals so these both piqued my curiosity. Like Dracones above, I was unable to find any firm info on Space Princess, but it reviewed well.
Stars Without Number, however, is available as a free PDF so I've got a copy of both the original and the revised version. I really like what I've seen of them (I don't like reading on the computer so I've only skimmed them). The revised edition has some 4e D&D elements that I am not a fan of (such as cherry-picking attributes for saving throws) so I'd probably go with the original edition if I were to run a SWN campaign. Even though SWN is class-based - something I do not normally care for in a science fiction game - the classes are loose enough and there is a skill system on top of the classes that allows a good amount of customization - not having played it yet, I do like the look of the system. And while SWN does provide its own setting, that setting is also loose enough and it provides rules for designing your own aliens, planets, etc. that are not as picky (from what I've seen) as in Starsiege so one could easily just ignore the provided setting/history and come up with one's own. Once my financial situation has leveled off, I do plan to invest in a hard-copy of Stars Without Number.
I also came across a game called White Star - another OSR. It is the Sci-Fi version of Swords & Wizardry's White Box Rules (which are based on the original D&D). Have not gotten around to picking up a copy yet but what I've read about it it's classes are based on Star Wars. Being an OSR it should be easily modified to whatever I'd want - but Star Wars isn't a bad place to start.
So, right now the front-runner in my quest for a science fiction RPG to suit my tastes is Stars Without Number.