Number Two/Maggie is a Posthumous Character who only appears in one tie-in novella and a couple of background cameos on the evacuation ship. However, her characterization as a nervous Bookworm and Camera Fiend who has learned some gymnastics and hand-to-hand combat to try and survive before her powers develop make her a memorable and endearing character who has a decent amount of fan art.
Nine's Cêpan Sandor is only in two prequel novellas, but he's probably better liked than some of The Chosen Many main characters due to being a carefree Brilliant, but LazyGadgeteer Genius with an interesting backstory that includes only becoming a Cêpan as a last minute replacement for Nine's original guardian.
Number Seven's human friend Hector is a particularly popular human character despite just being in one book. This is due to his status as a philosophical drunk who loves his mother and gets some Crouching Moron, Hidden Badass moments in the book's climactic battle.
Fanon Discontinuity: Sarah's death might be the one which fans have the most resistance acknowledging, especially ones who like to speculate what kind of hybrid kids she and Number Four could have.
He's Just Hiding: People like to believe that Devektra from The Lost Files may have survived the invasion of Lorien due to her Badass Bystander moments and cute interactions with Sandor. While the planet she was left behind on is apparently entirely scourged of life, some fans point out that she isn't killed onscreen despite ample opportunities when she could have been.
Sarah. It isn't that fans don't think she didn't die, but rather that they want to think she could have been resurrected offscreen.
The chaotic nature of the fight that kills Number Two's Cêpan Conrad and the underuse of the Cêpans in general causes some fans to wonder if Conrad is really dead.
Not even the interesting cepans, like Big Brother Mentor Sandor or Conrad (the only one assigned to a Garde of the opposite gender) last long, even though the first two could have potentially survived the death of their charges and been trying to atone for My Greatest Failure.
The greeters, the humans who met the Garde and helped hide them, would have made for some great characters but all are long dead and unnamed except for Malcom Goode and the traitor.
The original reluctant Les Collaborateurs editors of They Walked Among Us might have made interesting Redemption Quest characters if they'd showed up helping Mark run it.
Maddy (who is coerced into becoming a Love-Interest Traitor) and her father (an astronomer who discovered the invasion force and was taken prisoner) feel like they could have been explored more if not for them being executed after Nine was caught.
Number Eight is the only minority among the Garde, save for doomed Intro-Only Point of View character Number Three, and has some great powers and a charming personality. Fans were not happy that he dies in just his second appearance.
You pretty much expect it to be aliens or magic, but when they actually explain it, it's kind of sudden.
This is played for effect with the Mogadorians whose mouths are obviously not well suited for human speech, resulting in a mumble which sounds like baby talk.
Pretty much anything uttered by the Mogadorian Commander.
The appearance of the Mogs, especially the slits next to their noses which they apparently use to breathe.
Strangled by the Red String: It's explained that the alien race works like this, with your first love being for life. Number Four falls in love with Sarah within two days and apparently permanently. There's a long scene of overly-flowery declarations of love delivered in a manner that would make Padme and Anakin cringe.
And then he hands her over to Mark the Jerkass at the end before riding off with Sam and Number 6.
Visual Effects of Awesome: ILM were behind the special effects. Of course they're going to look spectacular.
They Wasted a Perfectly Good Plot: The movie could have been better if it were just Number 4 and Henri on the run from the Mogadorians
