Yeah, that was the simplified version of every bad guy we fought in ME1. You have to admit, there's a pattern. I remember that the Rachni that were bred on Noveria went psycho by being isolated from the queen, but I forgot what the whole deal with the Rachni wars was. I don't know anything about Ender's Game, though.
I think Cerberus' infamy is a result of them being a victim of their own success. They're a very idealistic organization with the best intentions for humanity and they refuse to acknowledge other authorities. This is prone to attract zealots with similar ideals but slightly more blurry moral boundaries. So they join an organization where they are told they're fighting the good fight and they make a difference, other than those bureaucrats who are blind to how things really are. Next thing that happens, your agents are feeding soldiers to Thresher Maws, still believing that this is the right thing to do, honest!
From what we know about the Geth, they seem to be quite indifferent about other races as long as they stay out of each other's business. Before Legion came along, I never really thought about the Geth as just another galactic race, trying to make it as they go along. That doesn't make them the good guys, only self-preserving. Like Cerberus, you might say. When on Tali's mission, I faced the choice of handing over the evidence and get her father erased from history, or withholding it from them when they might need it. But I never realised what implications it might have for the Geth. They won't like it if the Quarians just come waltzing in one day being all "Hi thar we'd like our planet and our robot workforce back now." Thinking back to how it all started, it really is conflicting for both sides. If you had a robot army as a workforce and a military force, and they became intelligent, would it be immoral to continue to use them for hard labor, that which they've been made to do and have been doing all their existence?
You're right about the grey morals between the races. I think they've executed it a lot better than Bioware did in Dragon Age, which was advertised to be morally ambiguous. The backstory seems much less forced and artificial in Mass Effect than it does in Dragon Age.