Okay, I'm going to say what a lot of people seem unwilling to.
I don't consider Joker a writer's pet because I liked Joker. I found him amusing and always rushed to talk to him at every opportunity. I suppose some people didn't, and that is their right. I can see how Garrus can be annoying if you feel like your Shep wouldn't like him. Honestly, all characters are kind of forced to be your friend one way or another, so this treatment of Tali, Joker, Anderson, Liara, Vermire survivor, ect. can hardly be called pet behavior since everyone is your friend no matter what you do. Hell, even Jacob is nice to you even if he cheated on you and you are ultimate **** to him. Side note- FemShep in ultimate **** mode is apparently pretty tame.
I think that Liara is a pet character, but I like her a lot more in ME3 than I did in one or two. In one she was about as interesting as a ball of belly button lint. In number two she was now some kind of amazing badass information broker or something. That was jarring and it felt like the writers knew exactly where they wanted to go but weren't sure how to get there so they just skipped two years. At least Garrus gave a little forshadowing that he was frustrated with the rules at C-Sec and was in favor of a little bit of killing of Saren. Him becoming a vigilante in number two didn't come out of the blue.
At the end of the day, characters from ME1 received much more attention and time in ME3 than anyone who appeared ONLY in ME2. ME2 exclusive squad mates in ME3? Nope, not a one. ME2 love interests? Take a look on youtube. The "romance" with most ME2 continued L.I.s can be summed up in about 5 minutes out of 30 hours of game play, some less than that. This wasn't helped by the fact that some of the ME1 squad mates are very boring. In my opinion I just don't care at all what happens to Kaiden or Ashley. I didn't care what happened to Liara when I started, but by the end of ME3 she was one of my favorites.
Kai Leng annoyed the hell out of me. I hate it when characters walk around like they are hot **** out of nowhere. I had never seen or heard of him before and all of a sudden he's unstoppable. I got mad every time I saw him because I wanted my Shep to stop dicking around and just shoot him. Oh he has a barrier? Good thing you shoot through barriers all the time in combat so that shouldn't really phase you much. Shoot a little faster, please. Oh, you're just going to stand there and watch while he stabs your flying car? Okay, sure that's fine too. Oh he has a gun ship? Please, Shep has shot down more gunships and other air devices than an anti-air canon. Just overload the shields and 3 shots with the Mantis will blow that thing... what, you've never seen or encountered glare before. Thwarted by the sun? Really? **** Kai Leng. So happy when he died. I wanted to stab him twice.
Damn, that was a lot longer than it needed to be.