So S2 was kind of a mess.
I so dislike that they made Moriarty a mother as a shortcut to make her vulnerable—no fucking way she doesn't terminate that pregnancy. But at least they left her ambiguously evil and potentially messing with Sherlock's head; please let's keep her that way, because she's so much more interesting, unless we get a really long extended arc justifying the change, which seems unlikely on a practical level. (Also keep her having a see-it-from-space crush on Joan, that portrait, oh my word.)
(Also: I don't care what kind of electronic monitoring they have on her, there is no way that she gets glass jars for her paints while in prison, nuh-uh, never, trust me on this.)
If we got told that Bell's injury was definitely fully rehab-able then I forgot it, which made me want to throw something at the screen when Sherlock told him he just had to work harder.
Mycroft. The thing with Mycroft is—it's not just that I do not find him attractive, because there are many, many people I do not find attractive. It's that I find him so unattractive that he is like a Dementor for my libido. Every fiber of my being recoils at the idea of him in a sexual context, and thus the whole Mycroft/Watson plotline made me want to throw a brick through the screen and run away shrieking.
Even beyond that, though, it was terrible because it made Joan a bone for the Holmes boys to fight over, and even if Joan pushed against it, Sherlock was still being an insecure jerk with boundary issues and I prefer to like Sherlock, please. And Sherlock's decision to work with MI-6 in the finale is way too rushed—I can trace the logic, but it deserved more, and again: you're being a jerk, Sherlock. Stop that.
And now for S3:
I was really not excited by Kitty at first because I didn't put it past the show to make it a tug-of-war over Sherlock's attention, which, ick. But now they're co-mentoring her, which is great even if I side-eye some of the details (Joan insisting that all rape survivors need to go to support groups; Sherlock being kind of a shitty mentor to Kitty early.). Also new boyfriend is cute and I really want evil drug lady to come back because that first episode was fun. So, I'm still not thrilled with Sherlock, but I'm a little more hopeful.