Sherlock didn’t realize what he meant to John until the “best friend / best man” scene in The Sign of Three. 

(Sherlock Meta by cosmoglaut)

John: I wanna be up there with the two people that I love and care about most in the world. Mary Morstan. And... You..
Sherlock: So... I am.. In fact.. Your... Best...
John: ...man!
Sherlock: ..friend?
John: Yes? Of course you are. Of course, you're my best friend.

This sequence is funny and sweet, but demonstrates a few things so clearly and painfully.

John plays incredibly close to the chest about his feelings. He apparently never explicitly told Sherlock what his role in his life is, or how important he is, preferring to let actions speak louder than words and assuming his meaning is clear. To everyone else, it is clear.

John severely overestimates Sherlock’s ability to understand how anyone feels about him. John makes a lot of assumptions about Sherlock’s emotional maturity and abilities, all of which are apparently wrong.

Sherlock has stupidly low expectations of how people he loves feel about him. It’s a bit hard not to launch into a consideration about Sherlock’s sense of self-esteem at this point. It seems fairly clear that Sherlock’s sense of self-worth must be based entirely on his intellectual abilities, to the point of sticking his fingers in his ears and humming to drown out anything else.

This conversation may be the core motivation for Sherlock’s actions for rest of the series. All the emotion, all the sacrifice, all the wrestling inside Sherlock’s heart, the beating down the doors of his own life and then throwing it away again, is all because of this conversation. The impact of which John continues to radically underestimate.

These two are so far from being on the same page, I’m not sure they’re in the same library.

And I think the deception of The Reichenbach Fall is the motivation behind John’s action throughout the series. The impact of which Sherlock radically underestimated. This begs the question: what did they think their own place was in each other lives? What did Sherlock think his role was in John’s life? A mere provider of danger fix? And what did John think his role was in Sherlock’s life? A mere side-kick? In a way both of their actions were fueled by the same thought which does put them the same page: “He won’t miss me.”

From a couple of angles, I was thinking that the next series has to be about John’s character development. And now this gives me another reasoning. It’s only after coming back from the hiatus that Sherlock understood what he meant to John. So in the next series, I believe, it will be John who will understand where he stands in Sherlock’s mind.

It’s like they are sine and cosine! 90 degree out of phase! You look at them and never know who follows whom. So question then is, what will force the phase shift and make them in sync? If all this reading holds, then the underestimation is the driver of out-of-sync behavior. Ivyblossom did ask earlier: what would it take for these two to actually hook up? Well then here is one answer: stop underestimating your own place in other’s life. How? Well… I don’t know. Yet.