I found it very weird that I had to do a loyalty mission for Garrus in ME2. I'd already DONE his loyalty mission in my own eyes, darn it, in ME1. We became squadmates. I helped him with his issues, tracking down his nemesis, etc. Then in ME2, I was really taken aback that Garrus wasn't "loyal." I do feel that those who did ME1 should have been given "loyalty credit" for Garrus, although I did enjoy his loyalty mission. I just hated having to earn the loyalty of who I felt was one of my Shep's most loyal friends all over again.
On Thane, as a Thanemancer, I didn't mind that Thane died in ME3, although I will never play that version again, preferring the modded version.
I was just so angry at the way it was handled, and much of it was very out of character.
The Thane in the hospital basically breaks up with femshep and then ever after has nothing to say to her at all. He's honestly quite cold and just says "we knew it had to end," whereas I just don't agree that this is consistent with the guy who found a new lease on love and life in ME2 (nor do I feel he would dump Shep and resign himself to a hospital).
And nobody ever mentions or talks about Thane, nobody mentions his situation, nobody asks Shep about him (shoot, when she romanced him in ME2, it was the talk of the ship, garnering discussions from Mordin, Kasumi, Kelly and others), and when he dies, nobody says a damn word. She isn't given a paramour achievement even if faithful to him and making out with him in the hospital, and in the original version, there was no final vision of him (at least the EC fixed this). Even the Citadel DLC content, as lovely as it is, rubs me the wrong way because it just feels like someone went, "Oops, we forgot Thane was an LI, here, feel better?"
Continuity-wise, I was also very irritated at the subtle and (I felt) OOC choices for Legion. Most of his major dialogue with Shep in ME3 is, "Oops, I lied about that, I knew you would be upset," and to me, that just doesn't feel appropriate or realistic.
I also disliked the ME3 handling of Kasumi (it felt haphazard and sloppy), Jacob (I just don't think he would have cheated quite so egregiously with NO word to Shep at all -- I don't like Jacob myself, but he did seem irritatingly honorable in ME2) and even Mordin. While I was touched at Mordin's death in ME3, I don't quite believe the total flip-flop he does on the genophage (nor do I agree with his new take that it's a priority now, and one worth dying for).
I think part of it for me is that I'm biased. I loved ME2 so much, I loved that squad, I loved that they were these mismatched damaged people finding new hope, comradeship and relationships, and that they were willing to die (flaws guilt and all) on a mission no one would ever appreciate. So for ME3 to arrive and spend so much damn time and attention on ME1 romances while jettisoning most of those squadmates and connections really made me sad.
On minor characters -- I thought Chakwas was very true to life, but I kind of loathed Ken in Engineering. Where he'd been charming in ME2, in ME3, most of his anecdotes are kind of coarse and gross and super-sexist. Did anyone else catch this?
Actually, same with EDI. I loved their evolution in ME2. Loved. When EDI called him "Jeff" after the crew had been lost, I was so moved. But the sexbot was just ridiculous, the outfits on her were ridiculous (as was the body on her, like, come on, talk about pandering to the lowest denominator), and I was actually embarrassed that I'd ever had a crush on Joker in game 1.
The real missed opportunity to me is an EDI who never got a body. I do believe Joker loves her and that she loves him (possibly even more), and that this developed beautifully in ME2. I just think it would have been more interesting and poignant for the story that instead of Joker going, "How do I have sex with a robot?" that he fall in love with EDI and go, "Okay. You know what? I don't need to have sex, I love her. We're there for each other."
But ironically, despite this, to me EDI is one of the better-written characters in ME3, and she does have a poignant and clear evolution. When she begins to determine her own outlook, philosophy, and moral code toward the end of ME3, it's really moving to me, and beyond that, Tricia Helfer voices her so wonderfully that she gives EDI a warmth and focus that make me love her in spite of her incredibly insulting sexbot design.
Anyway, I really love ME3 even if it sounds like I don't. But it felt characterwise like someone just read a bunch of ME2 flashcards:
Kaidan: single, devoted/creepy
Liara: single, devoted (yet curiously way less creepy to me than in 1, and LotSB actually made me like her)
Miranda: bioengineered, psycho dad, sister issues
Kasumi: Keije, thief, witty, sad
Mordin: scientist, helped doom the Krogans/genophage, sings G&S
Joker: Became friendly with EDI the AI (let's hook them up!)
Thane: dying assassin (what? there was more?)
I did think Samara's scenes at the monastery were very well-done and touching, however, and it was also fun watching Liara have to deal with the realities of Protheans.
Which brings me to: Javik. It's very very difficult for me to totally reconcile the Javik we meet with the sophisticated Prothean civilization we saw for two full games before. Honestly Javik is the one who seems primitive to me, and I do wish he grew at all -- he seems to progress very little during the game, and it's kind of depressing to view the game through his eyes. I would have liked for Liara or Shep to have affected him more, even a little. To give him some kind of hope.