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.
The Childlike Empress: Between the time loop, everything we learn in The City of Old Emperors, and finding out that she'd drawn Bastian into a world that it became more and more impossible for him to escape from even if he was frugal with his wishes and didn't lose his mind without a single warning, it's not too difficult to read The Childlike Empress as the villain of the story.
She is supposed to be True Neutral, and give each user of AURYN equal chances. It's up to them what they wish for. Remember that good, evil, beauty and ugliness are all equal for her. Likewise, insane, mindless husk of an Emperor is just as valuable as an enlightened human being who understands AURYN's true purpose: both serve to tell a good story.
Bizarro Episode: Chapter XXI, The Star Cloister's only relevance to the plot is that Bastian loses Al Tsahir before its intended use. Not even the fact that Bastian brought Atreyu with him is even mentioned again.
Doorstopper: For a book that, at least in the English Speaking world, usually finds its way in the Children's or Adolescent's section. If Harry Potter is the daddy of young-adult doorstoppers,then The Neverending Story is the grand-daddy.
Jerk Sue: Bastian is the book's second half, a fully aware use of the trope. Atreyu eventually slaps him out of it.
One-Scene Wonder: The Childlike Empress actually appears in only three chapters. It's a plot point that no one can meet her more than once.
Painful Rhyme: Granted, it was translated from German and the whole thing is impressive considering the translator worked with what he had.
WHAT YOU ACHIEVE AND WHAT YOU ARE IS RECORDED BY ME, THE CHRONICLER.
Tearjerker: The scenes where Bastian discovers the truth about the lion Grograman, and sits with him so he won't be alone.
Artax's death. And he knows he'll die, but he can't find it in his heart to resist. So he tells Atreyu to let go and stop trying to save him so he won't drown too, then gently tells him to look away so he won't have to see him go under. Atreyu does, crying the entire time.
The ending, in which Atreyu and Falkor make up and part with Bastian and set out to tie up the story's loose ends.
Woolseyism: The dragon's name was Fuchur in the original German book. Apparently they changed it because it sounds like future in English. Or, if pronounced a certain way, an obscenity.
In the second film, Bastian randomly falls down a completely random chute and ends up in an underground room called "The Ship of Secret Plots" filled with odd fantasy characters who are never explained or seen again.
Designated Hero: Bastian in the third movie. The Old Man of the Wandering Mountains describes him as "a special young human, a voracious reader, with great imagination and extraordinary courage", traits that Bastian does not possess this time around.
Bastian never does anything with the power of the Auyrn in the third film and sits around hoping the problem will go away, while the bratty sister and even the villains use the power they are given.
Designated Villain: Bastian's stepsister in the third movie may be a witch, but she actually does something with the power she obtains, and while what she does with it is selfish, Bastian's calling her out for screwing things up falls flat since he could have avoided it all by actually doing something with it himself when he had the chance.
Also, she's part of why he wins the final fight, by using the book to give him super kung-fu moves. While he's still got the amulet and, as noted under Idiot Plot, still isn't using it.
Hell, even Jack Black shows more initiative than Bastian!
Over the next few scenes, everyone laughs at Bastian's hair, but to be honest, his hairdo looks completely ordinary and commonplace circa 2008. You could go to any shopping mall in America and see plenty of kids with their hair just like this. So, in fact, NeverEnding Story III was a trendsetter, and well over a decade ahead of its time!
Idiot Plot: In the sequel, Bastian is given the power to wish for anything and have it come true. That being said, the only reason he went on this giant quest was because he didn't have the brains to consider simply wishing away the entire conflict. Considering he didn't yet know there were consequences to making wishes, there was no reason for his behavior except plain thoughtlessness.
In one scene in the sequel, Bastian wishes a way into the witch's fortress, and a series of ledges appear for him to climb up. Halfway up, the ledges run out so what does he do? He says "I wish for a step, I wish for another, I wish for another step, and I wish for another step." Even if he doesn't know that he loses a memory each time he does makes a wish, it's still a hassle doing it his way and idiotic. How about "I wish for a staircase" or "I wish I was inside this place." The witch is understandably smiling with delight as she watches him piss away all his wishes and memories in one setting, probably thinking What an Idiot.
The third movie is much worse. Bastian leaves the Auryn out in the open in his bedroom, where it is promptly taken by Nicole. And towards the end, when facing Jack Black, Bastian actually gives into his "Fight me like a man" spiel, even though he's got the Auryn back, and could easily wreak all kinds of vengeance upon him. In fact, Bastian barely uses the Auron, even when he can just use it to solve the conflict at the very moment he arrives back to the real world, due to reasons that just boil down to "No, Bastian."
Rooting for the Empire: In the third film Slip, the villain, shows more initiative and charm than Bastian, who spends the whole film sitting around trying to hope his problems away. As a result, viewers tend to hope that he wins out in the end.
They Just Didn't Care: The third movie had the Fantasians making pop cultural jokes, yet they still have a fish-out-of-water experience at the real world. Also, either the third movie's timeline spans from the first day of school to Chinese New Year to Halloween, or they all happened at once (with Bastian going to sleep before Halloween). And Bastian's father suddenly doesn't know about Fantasia anymore despite the second movie.
As well as Fantasia characters exploring the human world for a change, as opposed to the other way around. Unfortunately, it's played purely for comedy and not very good comedy at that.
Heck, even the random changes to the characters could've worked if it'd been tied into the bullies getting their hands on the book instead of being random, it could've shown the damage they're causing.
Very little of the original cast returned for the sequels
The third film's villain, that's Jack Black. To be fair though, he's often considered the best part of the movie.
Julie Cox, who played the Childlike Empress in the same film, is an example of both this and Dawson Casting, considering that she was 19 during filming and a good four or five inches taller than Jason James Richter, who played Bastian. In fact, Cox is only slightly younger in real-life than Tami Stronach, the Childlike Empress from the first film — which was made ten years before the third.