Complete Monster: Jonathan, unlike his aunts, knows that what he is doing is wrong and doesn't care. He tortures and kills people for fun instead of out of necessity. He tortured Mortimer with needles when they were children and plans to murder him now that he has returned. He uses the threat of physical violence to bully both his aunts and Dr. Einstein into doing what he wants all without showing an ounce of regret.
Harsher in Hindsight / History Marches On: Mortimer's comment about how one of his ancestors "scalped the Indians" as proof of how crazy he was...in fact, historically whites DID scalp Indians throughout the various conflicts between them. However, since most white Americans didn't know these facts when the movie takes place, it doesn't break the Suspension of Disbelief for the audience when Mortimer tells this story to Elaine.
Nightmare Fuel: Jonathan. The fact that he's in a film where everyone else is just charmingly kooky makes for quite a contrast.
Special Effect Failure: In the outside scenes, the obvious backdrop of the Brooklyn Bridge and Manhattan is jarring to modern audiences.
Values Dissonance: The treatment of mental illness hasn't exactly aged well. Not only is mental illness mocked, but there's a strong implication that the mentally ill should be segregated from the rest of society. No one finds it at all surprising that the police want to involuntarily commit Teddy for a series of noise violations (sadly, was Truth In Televison at the time).