Big Spoilers of course.
Diana Allers...I wish had more lines. It was nice that she came into my cabin a couple of times or I would hear her going to begin a story in her room, but it felt like she didn't have anything overly important to say. In fact, I don't believe any of the crew really talk to her besides Specialist Traynor, which is a shame. Also, everytime I talked to her she would always say "Do we have a problem Commander?!" in a real loud voice. No, I don't have a problem, I just wanted to see if you had any more things to say! Jeez. Felt like Cortez had more to say than her.
Also, some of the NPC's on the ship probably could have had more lines. I hated how you could never really talk to Gabby or Ken when they got on board, and it felt like they didn't have too much to say (although I did enjoy convincing them to hook up finally). Engineer Adams was nicely done.
But its the other smaller NPC's that bother me. Those two woman guards that have names? Why can't I talk to them? They seem interesting! Also there is this one ensign I think that Garrus talks to that has a name, but again, I can't talk to him in conversation, and he only shows up like 2 or 3 times (one of those times being with Diana Allers I believe; the one where he wants her to pull a story). Dr. Chakwas never really had much in the way of dialogue, but when she was nearly crying to Engineer Adams about how she isn't OK with what happened when the Collectors grabbed her in ME2, why couldn't I comfort her?!
I do love the awesome memorial wall though, and the citadel is big once again. Leads to running around all over for 2 hours doing sidequests, just like ME1, which I kind of enjoyed. Also love how awesome it was for the characters to move around the ship and talk to each other. It sort of felt like Ashley didn't have too much to say though compared to everyone else, which is a bit sad.
Hate how useless the Journal is in this though. Sometimes I would question whether I obtained an item during scanning for a quest, but the Journal was not helpful in answering. Also some of the quests being a bit glitchy. I ended up doing Conrad's Quest before even really talking to him, so I was very confused. Also missed a whole conversation/cutscene on Tuchanka before the game spazzing out and not letting me continue so I had to redo the whole thing(no really too long, only lost like 20 minutes, if that). Kelly also never showed up at all in the Refugee camp no matter how many times I went. Was a shock to me that my cousin who played not only met her, but that Cerberus had killed her after the coup attempt! Felt even worse; had it in my mind that not only did I not meet Kelly, but that she died off screen for me without me even knowing!
But the death scenes are pretty awesome. I looked up what happens when you pick the Geth over the Quarians, and My God. If I had gotten that outcome, I probably would have started to cry, or at the very least been hugely depressed because I romance Tali. Its the music that really sells it. But some other nice emotional talks include Garrus and James seeing who did the most in the lives, Liara showing you that object which she'll leave for the next cycle and asks your opinion on your own entry, Garrus and Liara's final conversations on Earth, Grunt almost dying, hearing the Asari cry out as the Reapers land on Thessia, and of course, breaking Kai Leng's sword and proceeding to kill the son of a *****. Oh, and can't forget to make TIM shoot himself in the head. VERY satisfying.
Also, the gay romance between Kaiden and Male Shepard was done pretty well I think. I don't know how much it differs from Female Shepard though. Must suck for FemShep though: Jacob cheats on you and Thane dies. Unless you have Garrus, Kaiden, or Liara, it must seem like a punch in the gut. Though I guess that's why they made Traynor available, I found her to be pretty likeable.
Oh, and the card table on the crew deck? Why can't I use that?! And my Collector's edition Dog that roams around the Normandy, why does that not do anything (it can at least pick up some credits or something...). Its even more hilarious because Ken and Gabby complain about those two things specifically. Also, whats the point going below Engineering and the Life Support Room if the only things in there are the space hamster and models? At least the crew quarters Adams and Chakwas would talk there sometimes...
The most horrible thing to find out though? After Thessia, Joker tells you how he has a sister and dad on the colony Tiptree. The colony name sounded VERY familiar and apparently its the same colony that the PTSD Asari in Huerta Memorial Hospital went to. She met a girl there named Hilary who wanted to be a pilot? Had to kill her to stay alive? That was Joker's sister, and he doesn't know. He even talks to Liara about looking up his sisters name on a ship full of children, and calls says her name is Hilary. His dad had probably been Indoctrinated as well. I HAD NO IDEA. Blew my damn mind out of the water when I found out. Thank you GameFAQs message board!
Really, besides the very obvious reason for hating this game (which I won't say, you all know), all my annoyances and hate for the game are pretty small. The things that work though, work really well, especially the scenes with Reapers moving in the background.