Sherlock's behavior towards John when they first met seemed rather antagonizing. Sherlock can be rather insensitive, but he was being downright rude towards John when he was visibly upset. Sherlock does care about John, and it doesn't make sense that he would go making off-color remarks about John's mustache when he's obviously angry at Sherlock. I mean, even Sherlock knows it's not good to have your friends angry at you. It almost seemed like he was doing it on purpose.
John being kidnapped and almost killed is definitely part of this season's story arc. Charles Magnussen (the villain for this season) was definitely behind it. It remains to be seen whether he will be a single season villain, or a two season one like Moriarty. I'm guessing his reason for kidnapping John was to show Sherlock what he was capable of and that he can kill them at any time.
One thing I don't understand was who the villain was. It was stated to be an "underground terrorist network", but Lord Moran (the guy with his finger on the trigger) was stated to be working for North Korea. It could be stated-sponsored terrorism, but I wish they would be a little more clear on who this guy is working for.
I really don't like the timing of when they explained how Sherlock actually did it. They used a flashback (or flashforward, it's hard to tell) right in the middle of a high-tension scene. I would have much preferred to wait until John and Sherlock weren't about to be killed in order to find out how he survived.
I'll have to admit that Sherlock's plan was a lot more elaborate than I thought. I didn't really have my own theory on how he did it, but I didn't think it would involve 25 homeless people, several Doctors, and MI5. That seems like an awful lot of people to have in on the plan, which would increase the risk of a leak. Also, the fact that they closed off the entire street would make it even more obvious that something was going on. I mean, how did John not realize that his taxi was entering what was an otherwise blocked-off street?
I'm pretty sure the timing of the media clearing Sherlock's name was not coincidental. Mycroft must have given them that information when he knew Sherlock was wrapping up with Moriarty's network and would be returning to London. He simply arranged that so Sherlock wouldn't be harassed and discredited when he returned.
