I had noticed the lighting of Holmes, but I hadn't thought about there being a transition to equal lighting at the end.  
Also, I don't recall one of them being lit more than the other in the Diogenes Club scene at the front with the sign language, but maybe because it didn't warrant the significance for that to matter?

Interesting, though.  Well, I think even though Watson is with him throughout the episode, Sherlock does seem to realize more that "there's always two of us," that John will always be there to help him and such, and we see them chatting at the end.  So could be that Sherlock realizes that he is not alone, that John is there for him?

I've never really gotten into a movie or tv show before now deep enough to consider "oh that prop was placed there - why?" or "they MUST have filmed this scene from this exact direction, because..." It's fascinating both how much goes into making one of these episodes and how much fun we can have nitpicking them to death. They seem to me like little puzzles in themselves. (Maybe to keep us busy while we wait 5 years for the next one??? hehe) It's just fun all around!