- The Rachni queen: Release a potentially dangerous animal who's kind nearly killed everyone into the wild or kill an entire species. The logical choice would be to alert the council and let them deal with it.
- The start of ME2: Why would you work for Cerberus? In the first game they're set up as evil, vile assholes who are responsible for releasing Thresher Maws on a human colony. And as my Shepard had the "sole survivor" background, that Thresher Maw moment was most likely THE defining moment in his life, the reason he is what he is today. And you don't even get the option to ask why the hell he did it. He just goes on with the conversation with the Illusive Man, the man responsible for it all mind you, like nothing ever happened.
- The end of ME2: Destroy the station or give it to the Illusive Man. Ok, both have their pro's and cons. But when you choose to destroy it, out of all the great reasons for why you should destroy it, Shepard picks the dumbest, most cliché answer he can. "I won't let fear compromise who I am". Really? You pick that instead of all the other great reasons for blowing it up?
- The Council: Especially in ME2. You saved their lives, you gave them undeniable proof that the Reapers exist, hell you have your own Geth that tells them "it was not Geth technology", and they still deny everything. Despite all you proofed, despite all the struggles you went through, they still won't believe anything you say. Even after you save their ungrateful asses.