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.
Alternative Character Interpretation: Is Stitches just another Mook, or is the greatest henchman in any medium? Royal Pain is de-aged into an infant, and out of pure loyalty, takes her in and raises her as his own daughter. And once she's old enough for her powers to manifest, he willing resumes his old position as her henchman.
Stitches' boss, Gwen, is a veritable fountain of alternate interpretations: Does she have any memories of her time as Sue Tenney, or is she just going by what Stitches told her? Is she mentally 17 or 45? Does she pick on Layla just to be an Alpha Bitch or because Layla reminds her of where she came from? Did she genuinely love Will, or was he just a valuable pawn who'd be Pacified at first opportunity? Is she the inevitable result of the Fantastic Caste System, or is she totally out of line? You can find support in the film for all of these, and resolutions to none; perhaps the never-made sequels would have revealed some of them.
Awesome Music: The opening scene is set to "Everybody Wants To Rule The World."
Michael Giacchino's score, a good example being Royal Pain's Leitmotif.
Crowning Moment of Awesome: When the Commander gives the kids and Ron Wilson the hero award and actually refers to them as heroes. Made even more awesome with the "Well Done, Son!" Guy moment right afterward with Mr. Boy: "Oh, and Jonathan - whatever you're teaching these kids, keep teaching them... it."
Cult Classic: A surprisingly strong fanbase for a oneshot production unconnected to any of Disney's better-known properties.
Die for Our Ship: It happens, Will and Gwen being the most common victims. The weirdest are the Warren/Layla fics that bash both, when you'd think they could just as easily be used as a convenient Pair the Spares.
Draco in Leather Pants: Lash. He's quite possibly the least sympathetic character in the film, yet he has piles and piles of fanfics portraying him as some sort of sensual lover.
Ensemble Darkhorse: "Freeze Girl" is an unnamed character with no lines, yet she has her own character filter at fanfiction.net and more stories there than Gwen does. Lash also qualifies.
Harsher in Hindsight: In some of the promotional material, Warren was jokingly declared "Most Likely To Become A Villian""◊ in the Sky High yearbook. Then in the actual movie, it's revealed that Warren desperately wants to be a hero and live down his father's reputation.
Misaimed Fandom: Warren fangirls really like parroting the inspirational line he gives Layla at the Chinese restaurant, ignoring the quite blatant fact that this is a parody of such lines, as five seconds later it's revealed he's reading it off a fortune cookie.
Narm: The "Pacifier" thing that regresses anyone into a baby.
Narm Charm: If viewed as a spoof of ridiculous Silver Age villain schemes. And it would well, if followed through on.
Steve is also a semi-common victim of this, with his canonical preoccupation with the family name twisted into outright obsession. If Will is gay, he usually gets the obligatory designated homophobe role, too; one memorable fic has him throw Will out of the house upon discovering he's dating Warren, and Will's new father figure subsequently becomes, of all characters, BaronBattle. The story ends with Josie leaving him for Mr. Boy.
Shocking Swerve: A curious example. Gwen's sudden complete personality transplant from cool-if-somewhat-possessive girlfriend to Alpha Bitch had no buildup whatsoever, however, when considered with the film as a whole, a lot of seemingly arbitrary scenes that appeared to have no point suddenly make a lot more sense (the malfunctioning light fixture at the dance, for instance, and also Speed randomly walking in on Will and Gwen as they're about to have a moment). Amusingly enough, a number of reviewers claimed to have called this twist from the beginning, using the logic that senior girls never date freshman boys.
Special Effect Failure: During the cafeteria fight scene, you can see the plexiglass shields protecting Will from the flames as he crawls under the lunch table. To their credit, though, they did use real fire instead of CGI.
What an Idiot: Who was the fool that thought an individual with the ability to to bend technology and machinery to their will wasn't anything less than a powerful superhero in the making? Short sighted doesn't really cover it. This is Fridge Brilliance: If it was the 70s or so, technology might not have been to the point where it was as important/used the same way as it is today, and so the power wouldn't have been seen as being as good. Also, the hero/sidekick slotting is treated way too cavalierly. Being a Technopath isn't very flashy, after all.
X Meets Y: X-Men (specifically the Grant Morrison era, where a lot of mutant powers were... less than useful) meets Harry Potter. It was probably not coincidental that the film came out at the height of both Harry Potter's popularity and the superhero movie boom, ignited by, you guessed it, X-Men.
The Woobie: Mr. Boy. Sidekicks get little respect as it is, but the Commander, who is shown to be very nostalgic, doesn't even remember working with him and never mentioned him once to Will. A deleted scene shows that he was casually left behind, still tied up after the Commander and Jetstream first defeated Royal Pain.