EDIT: Cerberus is xenophobic, not racist. I am fully aware of the existence of Cerberus.
> Cerberus is a human-survivalist paramilitary group led by the enigmatic Illusive Man. Cerberus' core belief is that humans deserve a greater role in the galactic community, and that the Systems Alliance is too hamstrung by law and public opinion to stand up effectively to the other Citadel races. Cerberus supports the principle that any methods of advancing humanity's ascension are entirely justified, including illegal or dangerous experimentation, terrorist activities, sabotage and assassination. Cerberus operatives accept that these methods are brutal, but believe history will vindicate them. Nevertheless, both the Systems Alliance and the Citadel Council have declared Cerberus to be a terrorist organization and will prosecute identified Cerberus agents accordingly.
- In ME1 they're a rogue bunch of moustache-twirling villains who feed humans to thresher maws to find out exactly how much of a crunchy sound they make. You're supposed to happily shoot them on sight without the slightest care.
- In ME2 they're a cynical and wealthy "the end justifies the means" organization of human patriots who trample over ethics in pursuit of a greater good, such as kidnapping kids to turn them into biotics and give humanity an edge. You're supposed to feel conflicted and hate the means they employ while recognising you do need to work with them.
- In ME3 they're back to moustache-twirling, but now they're also a giant army trying to take over the entire galaxy, and worst of all they also have Kai Leng as a poster boy. You're supposed to treat them as the secondary but unambiguous villain of the story (even if in ME2 you role-played as a fellow human supremacist).
In hindsight, Bioware should probably have kept the ME1 version as cannon fodder and put Martin Sheen in charge of a different, non-moustache-twirling but still ethically questionable human-first organization. What they actually ended up writing was a narrative trainwreck.
(ME 1: Drew Karpyshyn) Cerberus thinks humanity has to have the techonological edge, even when it comes to crossing the ethics line, a simple "for science!" taken to the extreme. Even before you figure it out you expect a blackop like that to exist.
(ME 2: Karpyshyn & Mac Walters) We need a fresh start for players who didn't play ME1, Cerberus is a little more ambigious and the overall tone darker-er, still agreeable (given aliens' and human governments do nothing about it) or at least understandable line of thinking "we can't save everyone let's focus on our kind". Weak but not horrible.
(ME3: Walters) WE WERE REAPERS ALL ALONG. WE COMMON HUMANOID ENEMY NOW. ALSO MARTIN SHEEN.
After all, the question if it's right to use the resources of people you profoundly disagree with (if you do! You can be a mankind-first person in ME after all) if you have to to stop a greater evil is far more interesting than having all the resources you want without any strings attached.