I actually liked Magnussen quite much. As the whole episode, I loved the sequence after Sherlock was shot, and the one with John as a dummy was pretty dramatic too. My only complaint the reveal about the vaults was too obvious, and I was literally thinking "now you've got to just kill him and it's all fine". It felt a bit lackluster, but I had my expectations too high, like s02e01 high.
Oh, and I really hope Moriarty just stays dead. Andrew Scott is a great actor, but it would be just too much.
I still need to stomach this episode, but for now my rankings stay like:
A Scandal in Belgravia
A Study in Pink
The Reichenbach Fall
His Last Vow
The Empty Hearse
The Great Game
The Sign of Three
The Blind Banker
The Hounds of Baskerville
Overall, the seasons for me are ranked as 2 > 1 > 3, but the last one will probably grew on me.