well seeing how there's a common theme in most FF's about some giant evil empire/corporation/organization that is trying to utilize the "magical force" in that world, and that your characters are former associates of the bad guys -- I'm not surprised at all.

other similarities (off the top of my head):

FF1 and FF8 - weird unexplained time travel
FF1 and FF9 - black mages with pointy straw hats
FF7 and FF8 - supermilitary operations with weird acronyms that start with "S", and the main character has a giant...er....sword
FF4 and FF8 - your enemy is actually your friend being mind controlled by your real enemy