Sherlock and John didn't arrest her because they are not police - and no matter what she has done, John has feelings for her. Even Sherlock is prepared to shield her for John's sake.
Humour? It may be funny sometimes, but it is based on the books and there isn't too much humour in those.
I have no idea what you mean by: "Pity about Sherlock/John and Sherlock/Lestrade."
Or about Janine.
You think Sherlock and John are bi (sexual?) because you read and write fan fiction. Fan fiction writers tend to be obsessed with such things. Haven't you ever had a close friend the same gender as you, who you feel extremely close to without sexual attraction? Or even a friend of the opposite gender for that matter?
Has Moriarty returned? I didn't see him and really don't know what will happen regarding his message - was the message even from him?
I guess we'll have to wait and see - or make it up and write it down for other fan fictions readers.