I all, I think that it would be cool if one of the factions was a bunch of swashbuckling pirates that just wanted more. They could start out with any old civilization on any old planet then Skynet, Judgment day, Skynet builds a commander then boom. Space Pirates.. They can start with Cybertron with one of them that wouldn't be bad. I just don't care for this waking up with no memory of the past thing, it's not chaotic enough and it make for crummy imagining of things.
I do agree that the current idea of how everything comes about is a bit weak, I don't think your idea solves it in a better way tho. I think it would need a good campaign full of dialogue to achieve well, and that is something they have 100% ruled out in favor of the galactic war feature.
... I dont like the idea of pirates... to much of a joke (for my taste, i want my games a bit gritty and serious, with maybe a small tastefull joke trown in, but nothing as big as a "pirate faction" (Unless its a realy well done realistic pirate faction that dosent refear to itself as pirates, then maybe)).