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These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Helen is the true hero of the story. The film is about Helen's realization that the shallow domesticity she has accepted is suffocating her as well as the rest of the family, and at the end of the movie she achieves happiness by accepting her true calling as more than merely a homemaker. This is supported by the interpretation of Violet as the second lead. Violet grows as a person much more than her brother Dash. Violet frees her family from Syndrome both in his confines as well as the explosion which kills him.
Also, think about what really saves the relationship between Bob and Helen. Is it Bob realizing how important his family is to him? Or is it due to Bob getting back in shape, getting (apparently) a better job, and getting the chance to shine again as a superhero?
Ironically, there's a deleted scene where Helen and Bob are at a barbecue and a career woman there is dismissive towards her choice to be a homemaker and Helen absolutely flips out at her. This was inspired by the director's wife being mistreated by people when she chose to quit her job and stay at home to raise her kids.
Mirage: a genuine case of Even Evil Has Standards who turns good due to horror at her bosses actions... or a smug Hypocrite who happily assisted Syndrome's murders before getting squeamish when she saw the results up close and then started to worry about her own neck rather than anything else?
Syndrome: Was his ultimate goal of a world where "everyones super" because he wants equality, or because of the chaos people would cause with super powers? Or just another way to spit on the real hero's graves?
Big Lipped Alligator Moment: The "no school like the old school" scene is this for anyone not aware of that they are Frank Thomas and Ollie Johnston of the Nine Old Men. Even after that, the cameo's still pretty out of nowhere.
Edna Mode. ("And guest.") Also Kari. Syndrome became one to the Pixar staff; he was originally only supposed to be a one-shot villain for the introduction, but they ended up loving his characterization so much that he was upgraded to Big Bad status.
Someone set up a poll for the best Pixar character. Frozone came in third, only under WALL•E and Woody. Edna grabbed spot number ten. For contrast, Mr. Incredible got #13, with the second highest ranked Incredible family member (Elastigirl) being ranked #26.
Frozone's wife, likely due to her part in one of the best scenes in the film. Not bad for a character we never saw on screen.
Family-Unfriendly Aesop: The film teaches against Tall Poppy Syndrome and false accomplishments - pretending that everyone is equally special is wrong, because some people really are better at certain things than others, and trying to bring them down to the level of everyone else will ultimately only make everyone worse off. While "be who you are, not who others want you to be" sounds like a fairly family friendly aesop, the rather cynical implication is that people in general will always tend to envy you for being better than they are unless your superiority is immediately beneficial to them. It also gets a bit muddy when the same Arc Words ("When everyone is special, no one is") are used by both the protagonists to complain about artificial praise devaluing praise for the genuinely extraordinary, and the antagonist to describe his plan to democratize superpowers through technology, implicitly equating to the two (and framing the latter as villainous).
Fanservice: Arguably Helen/Elastigirl looking disdainfully in the mirror at how her costume makes her rear look. It's clearly meant to be nothing more than a gag, but it'd be silly to assume some folks didn't see it as this.
Foe Yay: Syndrome is beyond way obsessed with Mr. Incredible.
Violet is worried that their parents' lives — or worse, their parents' marriage — were in trouble. Dash, incredulous, looks at her and snarks that the villains are out to dissolve their parents' marriage. Three years later, One More Day happens in Spider-Man.
This even applies in-universe given that the villains essentially are trying to dissolve their marriage at points (mainly by trying to kill Mr. Incredible).
The teacher who calls Dash "a little rat" is played by the same actor who later played Linguini in Ratatouille.
Jerkass Woobie: Mirage in the second half of the movie. Buddy Pine started out as this in the beginning and then....
Late-Arrival Spoiler: You know the plot twist at the end of the movie? When Syndrome kidnaps Jack-Jack? Yeah, it overlaps with the "Jack-Jack Attack" short, and it seems everyone is perfectly willing to discuss it openly.
Several people called the Kari phone calls and subsequent Jack-Jack and Syndrome scene a bonus materials deleted scene for the DVD on first viewing of the film. Lo and behold ...
Moral Event Horizon: Syndrome doesn't know at first that Bob's family is on the jet he launches missiles at. But when it's revealed that there are people Bob cares about - and that there are children on board - he still refuses to call off the missiles, mocking Bob and laughing at his anguish. He's also responsible for the deaths of several super heroes for his experimental robot, some of which were at Bob's wedding.
Mr. Huph smiling and saying "Well I hope we don't cover him" when seeing a man getting beaten and mugged outside his window, then threatening to fire Bob if he ran out to help. Needless to say, his getting thrown through a wall and several cubicles was extremely satisfying.
Ron the Death Eater: Helen gets some flak from some fans because of her being so against the Parrs using their superpowers and living like a normal family, ignoring the fact that superheroes are no longer allowed to be super, so them showing off their powers would result in them having to change their identities and move again—and it's implied that Bob's moonlighting has already resulted in this, which puts a lot of strain on their kids.
It also was considered by some to be a Lighter and Softer adaptation of Watchmen, because of the superheroes having to register with the government and go underground. Consider also the major plot point near the end of both: The Big Badattacks New York with a giant, octopoid monster. Also, it gives the same reasoning for not wearing capes.
Uncanny Valley: Downplayed by the animators intentionally giving the characters cartoonish proportions.
Also, the animation designs were a shout out to the Rankin-Bass "puppet-toons" of the 60s. Syndrome in particular looks more than a little like Heat Miser.
Unfortunate Implications:Cracked.com had an article arguing that the true messages of this movie are "the strong are strong, the weak are weak, and evil happens when you try to make the weak strong." They compared Syndrome's desire to give everyone super powers to technology being used to help the disabled. This is forgetting/ignoring the fact that Syndrome's evil plan was out of spite for Mr Incredible, rather than the goodness of his heart.