Moral Event Horizon: Doris gets one when she brutally murders Carl in order to steal the memory machine back. This foreshadows what happens to the future as a result of her and Bowler Hat Guy changing it very well. Fortunately both of these events get an in-universe Ret Gone.
No Yay: People pair Wilbur and Lewis. The weird time traveling incest doesn't put them off.
The Problem with Licensed Games: Averted with the home console version, which is a rather good action adventure game that is a prequel to the movie, and the Nintendo DS version, which is a third-person shooter with a simplified version of the console game's plot that's pretty fun but got flack for its short length. Played straight with the Game Boy Advance version, which is a mediocre game that switches between side-scrolling action stages and top-down puzzle-oriented stages.
Rewatch Bonus: At the science fair, Wilbur knocks over a box full of frogs and their owner makes him pick them all up. He isn't too pleased, calls her "annoying little girl", and she warns him: "I know karate". It's hilarious on later viewings when you realize the little girl is Franny in the past, Wilbur was calling his Mom an annoying little girl, and yes, she really does know karate.
Squick: Ummm... well, at one point Lewis is almost adopted by his future wife!
And he calls her "Mom"... which is not helped by the fact that the studio took Franny's character model and covered it with a cloak for use as Lewis's mom.
They Wasted a Perfectly Good Character: A whole family's worth; each of the Robinsons gets just enough screentime to see their persona, but not enough to really flesh them out. Mr. Enter compared it to a television pilot introducing characters with the assurance that they would get fleshed out in future episodes.
Trailer Joke Decay: Subverted. While Tiny's line "I have a big head and little arms!" was spammed constantly throughout the film's advertising, the gag stuck with a lot of people regardless.
Win Back the Crowd: After an abysmal five years, which included closing its legendary traditional animation unit, making a terrible first impression on the All-CGI Cartoon market and very nearly losing Pixar, Disney (and a little change in management. Thanks, John Lasseter!) proved to its fans that they were still capable of making good movies.