Another Sherlock Holmes reinterpretation: Holmes goes into fugue states where he becomes Moriarty and commits crimes. He doesn't consciously know about this double identity, but passively, information flows both ways. So Holmes believes that Moriarty is extremely clever because he's "always one step ahead of me, Watson, he was in this very apartment during the night!"
I continue to be fond of alternate takes on Sherlock Holmes, so here's another one:
Holmes is actually a network of experts hiding behind a common pseudonym. That's why he's considered a "master of disguise" - it's all different people. "Watson" is simply the codename used for cases where two Holmes operatives need to turn up to the same place. Think Global Frequency mixed with Sherlock Holmes.
It's long been fashionable to reinterpret Sherlock Holmes, such as in the recent TV shows Sherlock and Elementary. Apart from changes in time, place, and mood, the exact nature of Holmes and Watson has seen various permutations - here amusingly referenced by Kate Beaton. So here's my cynical take on things: Holmes as a fig leaf for corruption.