Ok I don't tend to like many 'James and Lilly survive' fics bit this on is pretty well done.
I do think that it doesn't make all that much sense for Harry to spend that much time with Ron and 'Mione compared to those in his family (Nim, Daphne), new friends (Hannah), and house mates (Padma and Penelope). He tolerates Ron because of Ginny at best and he barely even knows 'Mione... what's going on?
Author's response
Thank you for the comment! In actuality this chapter is the only one where Harry, Ron & Hermione are isolate together. Harry is a good person, so he's the only one who even cares to remember that Hermione doesn't know about the troll. Ron is the closest friend around and happens to be the reason Hermione was clueless. Harry dragged him along to take responsibility for his action, never imagining that they'd actually cross paths with the troll, after all, the girls' bathroom is no where near the dungeons. They become more scenery characters after this defining moment and Harry's closer friends take on the rest of the way. I just needed this moment to cement the Ron/Hermione friendship, that dynamic is perfect for the small moments they'll appear in future chapters. I hope this answers your question.