Ass Pull: John Carpenter himself admits that while writing Halloween II, the idea of Laurie being Michael's sister came to him "at 2:00 in the morning in front of a typewriter with a six pack of beer."
Broken Base: The theatrical cut vs the television one. The TV cut inserts some deleted scenes and eliminates some unnecessary gore - with some of the restored scenes explaining a lot of Fridge Logic from the original. But it also re-orders some scenes around - often clumsily - and fans can't agree on which version is better.
Contested Sequel: Though it's certainly one of the better received sequels, some people felt that the twist that Michael is Laurie's brother downplays his character to a degree. However, a lot of Michael is still a complete mystery, so the twist is acceptable for most fans.
He's Just Hiding: Jimmy. It helps that he survives in the AMC cut of the film. Not to mention that his last name in the script is Lloyd...which is the same last name that Jamie has in the sequels. This has led to some minor Fanon that Jimmy is her father.
Fridge Brilliance: Why are Michael's kills more violent in this film? Well, he got stabbed in the neck with a knitting needle, got poked in the eye with a hanger, got shot SIX times with a revolver, and fell of a balcony. Also, he's probably tired from chasing Laurie. So frankly, he's a little pissed.
When Jill is being stabbed and Michael lifts her in the air, it cuts to a shot of her shoes falling off her feet. This makes it slightly more comical than it needed to be. She looks less like she just got stabbed and more like Michael is giving her a wedgie.
The fact that Karen speaks to Michael thinking he's Budd for so long makes the scene funny rather than suspenseful.
Rescued from the Scrappy Heap: Marion Chambers proves more useful than she did in the first film, filling Dr Loomis in on a vital detail about Laurie and summoning back up in the climax.
The Scrappy: Karen not only arrives late for work but almost immediately leaves her post to fool around with her boyfriend. She's the nurse on a maternity ward! It's hard to see her death as anything other than Laser-Guided Karma.
Jamie Lee Curtis is clearly wearing a wig that only vaguely looks like her hairstyle from the first film.
Near the end of the film, Laurie shoots Michael in both of his eyes. However, despite the blood dripping, you can still see that Michael's eyes are in perfectly good condition through the eye holes of his mask.
Squick: The kid with the razor blade stuck between his teeth, presumably from when he bit into an apple given to him by a so-called "Halloween Sadist."
Too Cool to Live: Dr. Loomis. That is, if you follow the H20 timeline instead of Jamie Lloyd one.
Villain Decay: The revelation that Laurie was Michael's sister. Some felt that the reveal took away the menacing mystery that made Michael such an effective villain as it gave a reason for him to stalk Laurie instead of leaving it as an unknown motive. Others felt that Michael's obsession with killing his family members may make him out to be one of the more brutal or irredeemable slashers as even some villains care for at least one family member. This is still a rather divided twist to this day, but for the most part, people seem to accept it as canon as it's used again in the remake.