I'm not sure when most of the current Sherlock fans joined the fandom but based on a few posts I've seen it seems like a lot of people joined after the episodes had all aired or somewhere around when the last season was airing, which is why I think a lot of people don't know or didn't experience the way the series was received as it aired season per season.
To give context John's blog in the series was a real blog you could visit and they posted content on there alongside the episodes. this meant that the fans at the time actively read and posted about the blogs content because it was essentially a part of the series and how we survived during the hiatus between s2 and s3. So a lot of what is known about John is from the actual posts on his blog and the snippet of his CV we see in the series, the fandom also used other sources, like the original ACD stories and other adaptations to create what we 'know' BBC's John Watson as as a fandom.
I think we can say that we know so much about Sherlock and so little about John because John is the narrator of the story, he is telling the story of Sherlock Holmes so it stands to reason that we actively learn about Sherlock, John's not going to reveal much that isn't directly relevant to Sherlock or Sherlock's deductions of him in the series.
Anyway, I know the original post is a few years old but thought I'd clear up some of the questions for those interested!
Where did he grow up? What has been of his family?
Based on John's CV from TBB we can see he went to secondary school in 'King Edward Grammar School Chelmsford' so we know he lived somewhere around there from the age of about 11.
Sherlock deduces that he doesn't have an extended family in ASiP and in shooting script for TSoT it mentions John's Mum is dead, but the line was cut from the episode.
Who the fuck are Stella and Ted?
The first time we hear of Stella and Ted is when they comment on John's blog congratulating him on his engagement announcement.
Based on this comment on another of John's (or well Sherlock's in this case) posts they are and older couple. Considering they're calling him 'Johnikins' and 'darling' as well as sending a telegram to the wedding it is safe to assume that they know him pretty well.
Sholto pops up from thin air.
Yes, he does. But that's sort of where S3 and S4 initially fall down, characters and plot lines are introduced that don't make much sense. I think Sholto being dumped into the series with no indication of him at all beforehand is simply down to bad planning on the creators side. He is however a nod to the ACD character Major Sholto.
Why does he have trust issues, right from the start?
I don't know much about war and soldiers but I guess if you've lived in an active war zone where you are on high alert all of the time and anyone you come across could very easily kill you, it's probably not all that surprising that he has trust issues, although that is assuming he didn't already have trust issues before joining the army. He's probably just Those are just my thoughts though, theres nothing in canon that says why he has trust issues, as far as I know.
Harry has no face. But what about Clara? We know that John was angry that they broke up. Why?
Harry has no face but we do know, based on Sherlock's deductions in ASiP, that she is an alcoholic. She doesn't care for her phone, it is scratched from being in the same pocket as keys and coins even though it's practically brand new, it was also a present from her wife so you could say she's not very appreciative or takes Clara for granted. He also deduces that Harry left Clara and that John has a problem with Harry, 'maybe you liked his wife, maybe you don't like h[er] drinking', Harry certainly thinks John had a thing for Clara based on the comment below about the way he used to look at her. So it seems that John was fond of Clara and didn't approve of Harry's treatment of her which most likely stems from the drinking. We also know from these comments that she is 36 in ASiP.
Some of you spoke about the wedding but… do we know who is those friends that John joined for his birthday that Sherlock was not confident enough to stay around? * you know the birthday party of Lestrade' s video in many happy returns*
We do know some of the people who went to the birthday dinner, John posted it on his blog.
Now, out of the people listed there the only one Sherlock might have had a problem being around is Harry, but the other thing is John mentions Sherlock didn't come because he 'struggled to fit in', I'm not sure what we can take from that as he did okay with most of those people when they had the Christmas get together in S2, although he did sort of cause Jannette to break up with John by confusing which one of John's girlfriends she was, deduced Greg's wife was cheating on him again and called Molly out on her feelings for whoever she wrapped the gift for, so maybe he didn't want to go and accidentally ruin it for John. Especially considering John posted this post accusing Sherlock of making everything about him at that Christmas party.
Does he have friends beside Sherlock?
He mentions friends here and there in the blog, also one of his first entries mentions meeting up with rugby lads he was on a team with, for the people trying to figure out where the rugby player thing came from.
Why was he in Dublin the previous day of a scandal in belgravia? Vacation? Alone? Family business?
Can't actually remember if this is a fanon thing or actually canon, but I always thought he was away at a medical conference, maybe someone can corroborate this?
Bill Murray? Does he exist in this version? How did John survive? Did he know him before the army as in ACD?
Bill does exist, he commented regularly on John's blog. He's actually the first ever commenter on John's blog he comments on John's second blog post.
John also mentions him in the blog post the day before meeting Sherlock and tells us that Bill saved his life, but also the comment Bill left referring to the things John got up to before they went out to Afghanistan together, this doesn't tell us if he knew him before joining the army though, they could have met in training.
Mike…Good lad. What was their relationship? Were they closer before the war (because you know John is not very friendly when they met but was it his depression or did he put some distance between him and Mike at some point?)
They went to medical school together in Bart's, Sherlock deduces this in ASiP, John also mentions it in his post about meeting Sherlock.
John says they were 'sort of mates when we were students' which for a guy like John presumably means they new each others names, would chat occasionally or meet up on nights out but weren't actually close, so when John joined the army it's probably more likely they just drifted apart rather than had a falling out.
John not being very friendly probably has something to do with the fact that he's depressed and disillusioned with his life and he's sort of just a grumpy guy anyways. Mike also refers to John as being 'not the John Watson I know' which has him instantly on the defensive replying 'yeah, I'm not the John Watson...', it's probably hard for him to meet someone who knew him before his injury and to have them see him recently discharged and using a cane and his life essentially in shambles.
Every close person of his entourage are more related to Sherlock than himself. Like Molly (love her) is the godmother of his child. We never see them interacting even for a message without Sherlock in the room. And what happened to those relationships when Sherlock was "dead"?
Molly, Mike and Mrs Hudson all continue to post comments on John's blog as he wrote up some of the adventures that he never posted while Sherlock was still alive. John does mention trying to see Molly in reply to one of her comments, but we don't know if he ever did actually see her
We know he sees Greg at least once when he goes over to John's new flat to drop off the box of Sherlock's things that were left at the Yard, this is from the mini episode Many Happy Returns and John posts about it on the blog.
Do we even know how he met Mary??
Her first mention is when she comments on the blog, 7 months before he proposes to her. In the series she is a nurse in the same clinic John works at, so presumably that's how they met.
Why does he have already a problem with alcohol? OK his sister is an alcoholic but… why??? (is it canon that their father was alcoholic/ violent???)
It doesn't appear John has a drinking problem at all throughout the series up until TLD when he tells Eurus (as his therapist) that he didn't have Rosie the night before because it wasn't a good night and he can't always cope, it then cuts to a shot of him drinking at home alone in the dark and him continuing on to say he's letting Rosie down, all of this suggests that he is struggling with alcohol and using it to cope after Mary's death. John has stopped blogging altogether by this point so we don't actually get any of that extra information like we did with earlier seasons from his blog.
As far as I remember his father is never mentioned.
Side Note: I think part of the reason S3 and S4 felt wrong was because the writers lost the run of themselves a bit, but also they got sloppy. The Six Thatchers was already a case on the blog posted in 2011, this and based on interviews Moffat and Gatiss had given saying they would never touch things in the series because there was no need to, like Sherlock's childhood, kind of showed how far they had come from being meticulous with the details to the plot hole riddled and ridiculous back story series it became throwing in characters that have never even been hinted at but play 'massive' roles in John and Sherlock's lives.