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.
Awesome Music: The opening scene is set to "Everybody Wants To Rule The World."
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.
Designated Villain: Rare protagonist example. We're supposed to see Will as becoming slowly corrupted by his newfound popularity, and neglecting his real friends for people who don't really care about him... but then you realize that every instance where he blows them off was somebody else's fault. He missed his appointment with Layla because his parents insisted on dinner with him and Gwen, he didn't sit with them anymore after transferring to Hero track because Penny wouldn't let him, etc. He could have stood up to them, but that's really his only sin, and yet the movie wants us to think he was turning into a Jerkass.
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 temporarily regresses anyone into a baby.
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.
Unfortunate Implications: None of the female freshman we see are sorted into 'Hero' class. Admittedly Layla was only excluded because she refused to display her abilities out of principle.
Also, if you don't have powers, you are automatically designated as a sidekick. Essentially it means in order to be accepted in your own community, you need powers.
Will going out with Gwen, who turns out to be Royal Pain, who is quite a bit older than Will. Borders on paedophilia if you think about it. He even says after Gwen reveals she's Royal Pain, "Oh my God, I made out with an old lady!". Though it's strongly implied that the only reason she knows she's technically in her forties is because Stitches told her, meaning she's both physically and mentally 17, even with a gap of only three years the relationship has a lot of somewhat disturbing "experienced person taking advantage of inexperienced person" undertones, which, given that she's a villain, was probably the point.
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.
Possible 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.
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.