Living with Sherlock Holmes is difficult at the best of times. However well you know him and however much he likes you, he's a pain in ass to live with. He can't help it.
He has a number of bad habits, first among them his propensity for playing the violin when it's gone midnight. Normally John would be the first to admit that Sherlock can play beautifully (when the mood strikes him) but no amount of talent makes up for a sudden onset of very loud Vivaldi at 3 am. It just doesn't.
Second on the list is his total inability to be civil to anyone. Ever. It's not like he doesn't understand human feelings, because he's perfectly capable of manipulating them to his advantage, and it's not like he can't feel things himself (though everyone else would doubtless disagree, they weren't at The Pool) it just doesn't factor into his thought processes the majority of the time. When you're so busy connecting dots that no-one else can see, let alone draw lines between, a small thing like making Molly cry for the third time that month is scarcely a blip on the radar.
Thirdly, though this one moves up and down the list depending on the place and time it happens, is his habit of shutting everyone out and/or running off when he's figuring something out. John can understand why, and it's not like he can't admire a man who can think as fast as Holmes does, but when you're left standing at a crime scene, or in a London alley, or in a restaurant and your friend has just run out on the bill like he's being chased, it gets rather tiresome. And expensive.
There are many other things Holmes does that drives Watson mad, but last on the list that grows and shrinks depending on how charitable John is feeling at any given moment, is the talent the bugger has for getting under your skin.
He's had this conversation with himself many times- usually when he's traipsed halfway across London to hand the bastard the phone on the coffee table- and it usually goes something like this.
If he's so annoying, why not find another flat? There have to be other people in London needing a flatmate, who don't leave mould in the fridge on purpose... He can almost hear his rational mind breathing a sigh of longing. Find one!
But then the other half of his brain, the one he never really thinks about because it's usually so reliable, gives rationality a look of such contempt it shrivels up in a corner and tries to look inconspicuous.
And then what? Leave him on his own? It asks, with a sneer worthy of Holmes himself.
Leave him to Mycroft (whose not even there half of the time) and Mrs Hudson? He needs someone full time. Not a nanny or watchdog or bodyguard (like Mycroft would assign in an instant if only Sherlock would let him) but someone... comfortably in between. Because for all he's a grown man and can look after his basic needs (mostly) he needs someone to look after him. Someone to stop him, to calm him before he does something totally stupid, like saying something thoughtless that'll damage his relationship with Lestrade beyond repair.
John knows without asking that Sherlock would be lost without his work.
He needs someone, John knows this instinctively. He wonders, sometimes, how and why the majority of his understanding of Holmes seems to be instinctive, how the majority of their communication seems to be silent, in glances and unspoken humour. He doesn't understand how no-one else gets it.
He needs someone to translate and smooth things over with the Yard when he gets carried away, and bring him cups of tea at two in the morning when he's so wired up John might almost think he's using again. Someone to make him stop and wait and plan for a second before walking unannounced into the warehouse of Londons most infamous and violent drug gang.
It's not like Sherlock will ever thank him for this, and John doesn't really expect him to. It's that the feeling of relief when Sherlock finally stopped silently expecting him to move out still hasn't gone away. The grin he can't help when Sherlock's running at 90 miles an hour and the stuff coming out of his mouth is so bloody brilliant, is never far from the surface, and bubbles up at annoying moments.
And it's the pride he feels, when he sees the gleam of genuine humour in the eyes of the self proclaimed sociopath, he knows his mind was made up at 'Afghanistan or Iraq?'
He's staying.