I've noticed that too, from as early as TBB John doesn't seem to actually like Sherlock all that much, it's more like he tolerates him just to have the perk of crime scenes. It's sad really that it's played that way, that one of the great famous literally friendships gets reduced to John gritting his teeth. Yes, this Sherlock is more abrasive than he is in the books, and I like the fact that John is not at all bungling and fuddy-duddy, but it would have been nice to see a bit more genuine friendship between them that can't just be written off as a result of adrenaline. I get the impression that Sherlock, despite his casual insults, likes and appreciates John more than John likes and appreciates him. Really it's not that much of a surprise that Sherlock, ill equipped to deal with interpersonal relationships at the best of times, doesn't know he's John's best friend.
Martin plays John a bit like I imagine Martin himself, ie angry, passive-aggressive (at best), and spiky. Obviously I love the series and these versions of the characters, but I do wish he had dialled it back a bit, or that the angriness came out more at villains and less with Sherlock. It's funny in fic how often john is described as a healer and a protector, when we actually see little of either, especially in regards to his best bud. Perhaps TLD has poisoned me to John so I'm more inclined to look upon him unfavourably now, but I remember being surprised in TBB that he was already exasperated with Sherlock and was pretty confrontational. Perhaps you can guys can help jog my memory and point out scenes where we see John being genuinely nice and friendly when they're not in case mode (or drunk)? There have to be some scenes, but I'm drawing a blank. I guess because they spend so much time on crime scenes that's the only time there's any chance for them to be seen as friendly on screen. Bah.