Some of these have probably be mentioned already, but -
Kai Leng: My shields are down! Cover me while I recharge!
followed by
Kai Leng: There's only one way this ends. Target the supports.
I've raged enough about the Kai Leng fight on Thessia over the past 4 years, but it's still the mission I have the hardest time wanting to pick up the game to progress through.
Kai Leng: No, now it's fun!
The kind of line that someone liked writing, but that no one ever says ever when facing three to one odds. This type of interaction is why critics are usually so dismissive of writing in video games and, to be fair, in most poorly-made action movies.
FemShep to Jacob: I'm more interested in just talking for a bit.
To this day, I still want to ask Jennifer Hale if she was given direction to intentionally make that line as flirty as it comes off. I would probably have a higher opinion of Jacob had she said it more professionally, and it's unfortunate that I am judging Jacob based on how another character initially reacts to him.
Shepard to Wrex: The Krogan weren't ready for a cure.
Mass Effect 2 went out of its way in Mordin: Old Blood to give Shepard reasons to destroy the cure research based on how it was developed. This is why one of my Shepards destroyed it. So when I get to Mass Effect 3 and Wrex asks me why I destroyed the research, the dialogue wheel options were "I regret that I had do it" or "I stand by my decision." I chose "I stand by my decision" and got the above line of dialogue, which has *nothing* to do with why my Shepard destroyed the research.
Clone to Shepard: Drop your weapons or this won't end well for her.
Shepard: Alright..
My Shepard didn't drop her weapons when Captain Matsuo asked for them on Noveria. Didn't drop her weapons on Purgatory when Warden Kirul asked for them. Didn't drop them on Azure when Tela Vasir demanded them. And then....this scene. For the most part, the entirety of the Citadel main story is filled with moments like this. It is the DLC I want to play the least out of any in the franchise, including Pinnacle Station. Only the glorious moments of fan service that come after the main story push me through it.
Traynor/EDI tracks Kai Leng's shuttle to Iera system post-Thessia.
Really. That easy, huh? Especially considering that according to the vids you come across in Cronos Station, Kai Leng didn't go to the *IERA* system after Thessia. He went to Cronos Station, dropped off the Vendetta construct, had a chat with the Illusive Man, and then went to the Iera system. Considering that the signal would have ended at Cronos for a substantial period of time, it's amazing that Traynor was able to pick it up at all once Kai Leng left for Thessia, and unforgivable that she didn't make a note of where the signal stopped. Of course, all of this is supposed to be contingent on the idea that she tracked his movements through the Relay Network, which means it wouldn't have been possible to do once Kai Leng detoured in to the Horse Head Nebula. The trail through the Relay Network would stop there, and then Kai Leng's ship would have gone into FTL for the rest of the journey. NO WHERE NEAR THE IERA SYSTEM.
The whole Joker/EDI romance
Unnecessary, forced, and cringeworthy the entire time.