I respectfully disagree that this (concerns voiced by OP) is a problem. I do agree that it would be silly if we had characters from other FF games popping up all over the place, but I think it's a bit unrealistic to think just because Lightning showed up that everyone else from every other FF is suddenly going to be all over the place. Especially since I can only imagine that the story of Lightning being here would relate to the fractured reality of her world, which isn't exactly a running theme in all of the previous FFs. Either way, I think it's kind of a stretch to think anything revolving around Lightning or any other FF character would be anything more than a series of sidequests. It's not like the main scenario is suddenly going to be all about Lightning and Cloud and Sephiroth or something.

That said, I think one of the best things they could possibly do is make something like the Coliseum in The Void Beyond, somewhere you can fight characters from other places/times, which would give an opportunity to design battles against villains and hero parties from previous FF games. You could have everyone from the White Raven to Cloud and his crew to old school Garland. This would, incidentally, keep the "ridiculous fan service" compartmentalized so maybe fewer people freak out. Probably not, though.