Yaoi is a very profitable market and that is the reason why there's always many doujinshi that focuses on a yaoi coupling. There's actually a large percentage of doujinshi that isn't yaoi, but the more profitable yaoi ones seem to make its way here outside of Japan at ebay auctions.
Yaoi has been around much much longer than the emergence of FFVII, but Cloud X Sephiroth pairing is indeed popular.
I think an increase of yaoi might be felt outside of Japan, but in Japan, there is no increase of yaoi at this current time. It's just getting more profitable internationally.
Since you're into non-yaoi doujinshi, you may want to look into buying those comic anthologies of the Suikoden series. Those are bascially collections of many non-yaoi doujinshi.