I see no reason to lump FFVII in with anything else. Keep in mind that it's not just a section for FFVII, it's for the whole compilation. That's what? 4-5 games and a movie? I'd say that's enough content to warrant being on it's own since it at least makes sense to lump all the VII stuff together. Though it certainly made a bit more sense when there was a separate sub-forum for those spin-offs.
I'm also not opposed to the structure of the other sections really. I might wonder if we should combine FFI-III into their own forums since there's so little activity for them, but that might just make things worse for them. And I agree with giving XIII it's own section for now as well. There are too many spin-offs in that series and it's the most recent one, so it's at least somewhat justified. I also wouldn't want it's stink to rub off on any of the better games.
Aside from that though I wouldn't want to change the ordering too much. It's at least somewhat logical and consistent at the moment with groupings that make some degree of sense. Lumping the MMO's together would make sense from a genre perspective and as far as who's interested in them, but it might also make things a bit confusing for new members if the games aren't listed in numerical order. And I don't think I'd move the FF forums to the top. General forums are always going to be the most popular and frequently used no matter what we do. There's only so much interest in talking about older FF titles, and only so much we can still talk about years after their release. Yes, this is an FF forum and site, but that kind of discussion is still limited to a fairly small niche compared to the other forums. If Boko's idea was doable I wouldn't be opposed to it though. Failing that, perhaps we could occasionally bump an FF forum up to the top. Perhaps when a significant event is going on such as a let's play, or even just cycling through them to encourage some extra discussion.