This show is reaching "Heroes" levels of Death is only Temporary and at this point, you basically can't believe anything you've seen because of stuff like the bad guy's mind palace visualizing itself as if it was a Google Glass output is just a bogus misdirect. I'm really hoping that Moriarty isn't actually back and it was a plan by Holmes to make it so England needed him but I doubt it.
I'm not sure why it took Sherlock so long to realize that once Magnussen said that he didn't have the actual intel that he could just be killed. And his plan to frame Magnussen to get access to the vault was ridiculously simple and something Mycroft simply could have done ages ago.
Also, it seemed to be established that he had something on Mycroft for a while now but then it comes out that he didn't have anything until he had something on Sherlock, which was Waston, and thus Mary. But the "Don't cross me or I'll expose your brother's friend's wife is really a rogue CIA assassin which will just really break John's heart" threat doesn't really amount to much of anything.
Magnussen's lack of an evil plot also made his story lack much impact which was why they had to remind us time and again that he was so dastardly and the most dangerous foe they've ever faced. At least give us examples of things he did via blackmail that were so wrong. A businessman having undo influence over politicians? That's basically all modern politics is today. Is Holmes going to do battle with Monsanto next season (if there is one)?
They did do a good job of lulling me out of my There's Something about Mary feelings in the first ep but the ultimate explanation was lacking. I'm not even sure if she picked John for a reason or not. It doesn't seem like it was a compelling one.
I'm still in for another season but I have to say that I won't really be on the edge of my seat waiting for it or even broken up if there isn't another season.