So I love the series and just got my girlfriend to watch them all as well.  Now that I have mulitple viewings I've developed some questions and observations about the season 2 finale.  

The biggest issue in this episode is the apparent creation of a computer hack that Moriarty has developed that allows him access to everything.  Now before this episode we caught a glimpse of Moriarty imprisoned and being released, leaving a cryptic message of Get Sherlock.  Later we find out that Mycroft had imprisoned Moriarty because of the code and they couldn't crack him.  He apparently got him to talk about something by talking about Sherlock's history, but exactly what he said wasn't learned.  My problem with that is this.  Moriarty didn't reveal to the world that he had such a code until he commited the break in.  So how did Mycroft know Moriarty had such a code?  Did Moriarty start a rumour he had it?  Furthermore the idea that something as simple as a few lines of code breaking into anything is far fetched.  Moriarty reveals this at the end of the episode. It was nothing more than a few people paid off to help him make it look like the code existed. So why did Mycroft and the British government even arrest Moriarty?  There was no evidence of the code and it hadn't been "used" yet.  It would have made more sense if Moriarty had been arrested as a result of Irene Adler's cell phone being broken into by Sherlock.  Moriarty after all had contacted Mycroft to tell him he knew about the false terror attack in the first episode of season 2.  Irene had been in contact with Moriarty and no doubt had kept some sort of info on him to assist her in the future.  So as fall out from the cancelled operation the British government would have put pressure on Mycroft to get rid of Moriarty who had played a role in cancelling a large and no doubt costly operation.  But that wasn't the reason Mycroft gave for imprisoning Moriarty, it was the code.  Also why did they let Mori