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In series 2 Sherlock is the one who is scared and even horrified by the idea of feeling emotions. In ASIB he mocks Irene because she let emotions and feelings rule her head.
Sherlock definitely feels something for John (and both Moriarty and Irene know that) but he tries to suppress those feelings because he thinks they are just a weakness, a chemical defect (see his speech to Irene).
Somehow it is only fitting, and bitterly ironic that in series 3 Sherlock is the one who ends up "embracing" even the most destructive aspects of his emotions and, especially, of his feelings for John.
In TSOT we see that he puts John’s happiness in front of everything else, he tries to be the perfect best friend, he watches John leave even though it is clear that this is causing him terrible pain. And then, in HLV, he ends up killing a man for John, to ensure he can be safe, even if this means being sent to jail or on a suicide mission. And he ends up making mistakes, because of this display of selfless love for John. (Mary might still be a mistake…just saying. Does Sherlock really trust her? Or is it a bluff?)
On the other hand, John, the one who had acted in a more emotional way up to s3, seems much more guarded. He seems to be moving further away from Sherlock…maybe because the “Fall” is something that John has not fully overcome yet. But this at least apparent detachment is somehow artificial and pathologic (how can you not question the fact that your wife shot your best friend?). Something is definitely wrong.
John is living a lie, there's no way around it, and the normality he’s clinging to is just a facade (remember what Sherlock told Mary in Leinster Gardens?). Somehow I think John is acting in a way that by many has been perceived as "weird" because he’s overwhelmed; he’s trying to keep his word (wedding, pregnant wife, wuite a big commitment), he’s putting Mary first, but this is bound to backfire sooner or later because the wedding is based on a pile of lies, half-truths and convenitently overlooked things (personally, I don't think Sherlock's statement that Mary didn't really want to kill him makes much sense; it only indicates that Sherlock is downplaying Mary's actions for John's sake).
Indeed John’s detachment from Sherlock actually crumbles in some significant moments: when he remembers their first case together, when he’s asleep (dreams and nightmares are important with John, they were the first thing we saw of him in ASIP), when he sees Sherlock and Janine acting like a couple, when he sees Sherlock with the ring “for Janine”. There’s definitely something going on. But this time the one who’s trying to suppress his feelings for the sake of something he sees as more importart (in his case a possibly bad choice he made, Mary; in Sherlock’s case it was the work and his detachment from feelings and emotions).
In short, series 4 has a lot of work to do.