It would be hard to come up with a storyline for the Incredibles attraction. Although the movie did end with a cliffhanger of sorts, would Disney base a ride on that? Since the Incredibles ended with the "underminer," it could be like a journey to the center of the earth roller coaster like one of the international space mountains.
You're overthinking here.... THEY"RE SUPER HEROES!!!! And Mr Incredible and Elasta-girl have MANY VILLIANS who would want revenge from past butt kickings.
The Incredibles is for all intense purposes a Comic Book Movie!!! And COMIC BOOKS have different stories, villians etc.
The end of the movie didn't as much setup a cliff hanger as it showed that the FAMILY was now FIGHTING CRIME together... like a Familial Fantastic Four or Avengers. Its a crime fighting family.
Personally, a ride a la Spiderman would be PERFECT for the Incredibles. You can even correspond it with a TV show (something I am surprised we have NOT seen from Disney yet.). Even as a rollercoaster, you could easily incorporate everything...
Maybe something like this
Start the preshow or attraction with a premise of the Incredibles showing their powers OR Mr Incredible and Elastagirl being inducted into a Supers hall of fame. We are shown some of the hall of fame exhibits, the happy inductees, their families and friends, etc. The exihibits are of famous battles from the past, villians they defeated etc. We then realize that the villians are at the ceremony and just as we realize it all heck breaks lose. The villians take us captive and the family comes to save us and liek Spiderman, the fight is the essence of the ride.
All you need fromt he movies is the main protagonists. The Villians could be anyone.