Just saw the final episode for the first time yesterday. Loved it, obviously, and am now trying to put my grey matter to the problem.
I have a few thoughts on things I wonder might be relevant. I keep thinking if hints from all 3 eps point to the resolution to how Sherlock faked his death.
In Baskerville, I noticed that the doctor admitted that there were tests in human cloning - and when Mycroft talks of Irene's death he says only Sherlock could fool him. And we see, Sherlock has.
That leads me to believe that Sherlock KNOWS how to fake a death, including identifying the body - possibly DNA splicing or such.
Of course, it could be that Sherlock didn't know how to do this but Mycroft did (after all he had access to Baskerville long before Sherlock knew about it) and he helped Sherlock fake Irene's death for the authorities.
I do think Mycroft is heavily involves in Sherlock's fake death, and that does not necessarily mean that Sherlock went to him. If what Mycroft said about their interrogation of Moriarty is correct, he already knew of his obsession with Sherlock and likely that Moriarty would not rest until he was dead. He could even have known of Moriarty's plan (to a degree) and himself had prepared for it. I am sure he was not keen on Sherlock's publicity, and been quite pleased to help Moriarty discredit Sherlock as it fitted with what he wanted and he was able to protect Sherlock in the long run.
Another thought I had was back to the first Moriarty episode. In that episode he used other people's voices to speak for him, what if he continued to do that? What if Richard Brook really did exist and was an actor, but it wasn't Sherlock that hired him, it was Moriarty. either we never saw Moriarty or it was Moriarty some of the time and Rich at other times. As they said it is easy to hide lies in the truth. This would also allow for Moriarty not to be dead on top of that roof, only Rich has been killed - which Sherlock says is what he's going to do, kill of Rich.
Anyway just some incoherent thoughts.