I played the first game and wasn't impressed at all... I'd like to see a new engine, especially since the FF on Marvel Ultimate Alliance is so awesome... it's honestly going to be hard to top...
I'd go for a third person over the shoulder in a free roam enivronment controlling one FF member at a time, and the others being controlled by AI. Giving each of only FOUR main characters (with SS unlockable) a full suite of moves and their own gameplay style (Reed: puzzling adventure, Sue: Stealth Combat, Johnny: Flying Fighting 3PShooter, Ben: Hulk Ultimate Destruction 2) and then letting them loose on various enemies and situations with different weaknesses and solutions would be a grand idea...
Five to ten large levels (NYC, Latveria, Space (Station), Atlantis, Wakanda, Negative Zone, Atillan, etc) could not only offer explorable areas where 'fantastic' things can be discovered, but display a variety of the FF's history while providing villains and soldier-troops that are interesting, varied and challenging.
Then, with four well developed fundamentally different gameplay styles at your fingertips, you then introduce amazing multiplayer so that four people can link up online and cruise in the fantasticar together. Ownage.