I see games like Xenosaga don't really go into stories that don't in some way connect into the main plot, I mean even Pied Pieper was a pre-qual to explain Ziggy's past, and some more information on Voyager and Dmitri. Same with Kingdom Hearts. I think it's actually a very well done technique if done right.

Then there is a game like Suikoden who takes a different approach. I don't think they handled it as well as they could have, but you have Suikoden dropping hints and aspects of mostly unrelated things happening in the world (Or at least loosely related.) Luc is a pretty good example of this, as is Yuber. However, it has a tendancy to put these things in the forefront for periods, only to not explain it in game. Still though, for the most part handles expanding the world past the things that directly involve the main plot very well.

FF VII however? No. Just no. (Well, except Rufus was smurfing awesome in AC).

What I'm getting at is if they went in intending to leave things open for expansion it works, but when they try to add things where there wasn't meant to be something it can fail pretty badly.