I've been replaying Mass Effect and there's literally a side quest where a bunch of biotic "terrorists" have taken a chairman from the Alliance hostage. Specifically because he voted against reparations for L2 biotics, being an L2 biotic requires implants which cause insanity, mental disability, and crippling pain. So Shepherd is literally sent in as an agent of capital to kill them, and you don't have anyway to express any sympathy to the biotics. The paragon path is literally just telling the biotic leader that you won't kill him if he lets the chairman go, and whooooa as soon as you convince the leader to stand down, the chairman has a change of heart. This stood out to me cause it's just a small side quest, but the series both sides genocide and has you actually commit genocide in 2. The Batarians, despite the series trying their best to paint an entire species as xenophobic slaver/terrorists, are victim to multiple war crimes committed by the player character. The game has created a situation where there are 'good' aliens (the council races) and 'bad' aliens (batarians/vorcha/krogan) and the lives of the 'bad' aliens matter significantly less than the good aliens. You get hordes of vorcha and batarians to kill, and dialogue and story reinforces the fact that it's okay. There might as well be calipers in the game. It's honestly kind of fucked to play through.