Watching Woolie's LP of Mass Effect 2 and enjoying reading the details with a fresher mind. Ashley in 1 is widely derided for being a racist, but really that's just the sloppy writing; every sci-fi or fantasy type media got one of those, they're just not the equivalent of screaming the n-word in every casual conversation.
Cerberus in ME2 is far more insidious. By the time you start the game you're already well aware that they're "humanity first" and everything that entails - a fact that they never try to hide. But they also never say the quiet part out loud, that for humanity to be first, the aliens will be last. They're also an explicitly predatory organization; every member who joins is an outlier in some way, kicked out of the military, losing their families, being unfit for society, all people who are more than grateful for getting another chance - and quite a few have had traumatic experiences with aliens. Its a curious parallel to how real world extremist groups operate, providing a safe space for privileged people who felt wronged society and offering a larger, noble goal, at the same time they're cut from the rest of the universe from associating with such a shadowy enterprise.