I think that we have to assume that there were many conversations between Sherl and John in the months he was Hospitalised that led to John being reconciled with Mary.
I really can't account for John's muted goodbye to Sherlock - in my own little fairyland in my head, Mycroft had already assured John that Sherlock's exile wouldn't be for long, but I don't really believe this happened and it does leave a sad shadow.
(In that same fairyland, John will surprise Sherlock by naming his daughter Shirley:D)

The truth is that the writers have left enough gaps to go back and take the story in a different direction, I think.

Whether they'll choose to do so remains to be seen.

saturnR wrote:

I thought Sherlock did spot Mary. Her connection with CAM is a major reason why he takes on the case. He already had his suspicions about her earlier but because they found out that she was pregnant, he switches from protecting John to protecting his child.

In terms of the deduction itself. It's easier to deduce say being in the armed forces when the soldier has just come home from a war zone than it is to deduce that someone was a spy/assassin/con artist five years prior to your first meeting with them.

As for that conversation, yes I'd love to hear it in Series 4

I'm not sure which case you are referring to; Sherlock gets his client, Lady Smallwood, at the beginning of HLV, and he assumes that the person about to shoot CAM is Lady Smallwood. Indeed, he addresses her by name.

In view of Sherlock's accurate diagnosis of John's psychosomatic limp, I think that it was pretty impressive

Sherlock deliberately chose not to follow up 'liar' on his reading of Mary because he'd been horrified by John's reaction to him; I do accept that Sherlock had those reasons. What troubles me is that John doesn't ask why the second greatest deductive genius on the face of the planet failed to spot her, which seems to me to be what the John of the first two seasons would certainly have asked.

So yes; definitely need that conversation...

 

You're more than welcome to visit whenever you want to, Willow

tonnaree wrote:

I didn't see John at the airfield as "cold" but rather very repressed.  There are a couple of moments when he looks like he's may break which I found powerful if fleeting.
  I credit this to Martin's amazing face.

Agreed!

And I think John simply understands that Sherlock's deductive powers aren't infallable, and that he's human too. He made plenty of mistakes in previous episodes, including missing Moriarty. 

SherlocklivesinOH wrote:

I felt like John's "Is everyone I've ever met..." question WAS this conversation in a sense. Because it seemed to me he was directing his anger at Sherlock. It felt like he was asking, "Why didn't you warn me?"

 
It certainly could be read that way, and I shall do my best to try to do so in future