Well, lots of people like to contemplate (SPOILER)Necron, whose existence was vaguely foreshadowed in the game but came as a surprise to many.
There's also the V=D theory - basically, (SPOILER)some people aren't sure whether or not Vivi is dead at the end. Both of these can be interesting to contemplate from time to time, but there are fairly definite answers to both of them, unlike FFVIII's incessant R=U, or FFVII's "Jenova or Sephiroth?" debate.