User blog comment:SilencedSkies/The Illusive Man: Good, Evil or just bad writing?/@comment-4950455-20120730043106/@comment-4950455-20120730092140

Even taking that into account, everything still doesn't add up. The Cerberus of ME is described as an Alliance intelligence operation that recently went rogue; the Cerberus of ME2 was founded decades ago and never formally had any association with the Alliance. And while there are efforts made to justify other divergences, such as ME2's vastly increased resources, the entire thing still smacks of (another) retcon.

I don't dislike ME2's Cerberus, but it honestly feels like the writers would have been better, when creating their large morally-gray secret organization, to make up an entirely new group then to appropriate the card-carrying minor villains of the first game.