Morality isn't just black and white
In Episode 3 Obi-Wan said "only a Sith deals in absolutes".
An ironic statement because there's no middle ground in Star Wars, there's never any doubt in anyone's mind as to who's on the wrong side, a mere glance is enough to figure out which characters are the bad eggs. That guy in a black plastic suit? He's a bad-un. The hooded wrinkly reptile looking dude? Definitely not your friend. Saruman with a red Lightsaber? Don't shack up with him.
While the good and evil stuff isn't a bad plot foundation, we much prefer the doubts and quandaries that Mass Effect left embedded in our brains. Tearing hair out over decisions and constantly pondering over 'lesser of two evil' situations, there's no black and white here. The Reapers are the red - Shep knew that since Mass Effect 1 - but everyone else is a continuously shifting between shades of blue and red, it's up to you to figure out how you want to deal with people.