There was no problem with pre-split /a/, moot just happened to pay his yearly visit to /a/ when Mirror Moon released Utawarerumono, so /a/ was pretty enamored with it and moot got pissed off people weren't talking about anime more.
This lead to a handful of fags wanting to cause drama harassing moot to make new, personal boards for them - what moot doesn't understand is that for every one person who complains one hundred people are happy. So instead he decides to cause a lot of faggotry and split the boards up unnecessarily with unbelievably shitty criteria.
Anime, manga, visual novels, light novels, figurines and even Touhou are all interconnected, it's retarded to separate all of them since there's so much overlap in between them. "General Japan" is not a bad idea, but stripping /a/ of light novels and Touhou inherently was.
I was a Touhou fan since 2004 before those fuckers started the hijacks, only a small group of fags turned all of 4chan against Touhou and most of the other fans hate them and either stick with /touhou/ or quietly hone their craft in private.