Working with Cerberus, which is a big no-no to Alliance.
Working with Cerberus, regardless of alliance with them or not.
Of course, Cerberus. Stands to reason I guess.
Said moments aren't fitting of the tone or story. I don't mind tender moments with the LI and the idea of letting off some steam, but the humor was unfunny for the most part to me, just irritating and not my style of humor. We didn't really get to see any squadmates 'interact', if you can call it that. I'm not a shipper among the squadmates, but I wanted to see some conflict between, say, Ashley and the former Cerberus crew-members. I prefer things logical to emotional and campy every day of the week. I didn't want the story to go in a light-hearted, fun direction. I wanted it to be serious and grim. I didn't want my Shepard to react to the whole cloning thing as if it was like he found out he had some far-fetched admirer who he was embarrassed about. I wanted to see some legit meta questioning about identity and who and what he is. I didn't want to see the clone and company as far-fetched and silly, I wanted to see them as legitimately dangerous.
Re the 'Clone' plot - that didn't particularly bother me either way to be honest. I can see what you're saying about the meta questioning and agree that that would have been an interesting way to take things though.
In terms of the rest - the last thing I wanted the trilogy to end with was more grim dark. The ending to the overall narrative was depressing enough to begin with, no need to pour yet more on top.
Opinion on the Citadel DLC does seem to polarise, which is fair enough, it's certainly not going to please everyone. I'm just glad that I'm one of those that liked it! 