There is a scene missing from Ferris Bueller's Day Off where Jeanie finds Rooney's wallet in the house and gets so angry that she decides it's better to support her brother than to let Rooney get away with terrorizing her.

This could be done without letting the audience know her change of heart, but then afterwards her motivation would be clear.
As is, her decision has a bit of whiplash to it.

This leads to a sequel where Jeanie and Ferris reconcile, and he helps her have her own day off, probably pulling pranks on Rooney.

But sequel aside, the movie is also missing an end montage where characters reconcile, or have some catharsis.

Ferris' character is the biggest problem. Literally nothing happens to him. He ends the movie exactly the same way as he started.
He learns nothing, faces no consequences (despite inflicting great harm on his best friend), and generally gets everything he wants.

This complete lack of any arc has led to the fan theory that Ferris (and by extension Sloan) are figments of Cameron's imagination, where Ferris represents the end goal of Cameron's existential crisis.

So, the end of the movie is missing a scene that shows Ferris actually realizing... anything.
Which should be his relationship with Jeanie. Not sure how it would play out exactly, but Ferris realizes that he loves his twin sister and doesn't want to fight with her anymore.

Yes, Ferris and Jeanie are twins.

Jeanie would have the same realization, the groundwork of which was already laid at the police station during her talk with Charlie Sheen.

I would also have an end-scene where there's a shot of Cameron sitting down, his father walks in (we just see him from the back), Cameron stands up in front of his father, no words, and cut to black...

Sloan would eventually be caught by Rooney because, for crying out loud, it's not hard to find out if someone died, and she is severely punished. She blames Ferris and they break up.

Things spiral for Ferris from there, leading to his parent's divorce, rejection from college, maybe Sloan's or Jeanie's suicide, Cameron's alcoholism...

And I'm stopping this thread before it gets any darker.