Aerith and Bob: The author keeps some names from the original game, while changing others (largely to avoid Who Names Their Kid "Dude"? - see below.) Here we have Linda, Alexis, Enzo, Axel, Tim, Lucien, Marley, Lara, and Rocky. There we have Ansem, Braig, Vexen, Saix, and Xion. Such a mix.
Alien Sea / Alien Sky: At the start of Episode 6, Tim realizes something's hinky when the sky is suddenly red, and there's no school across the street - just impossibly beautiful blue springs.
Artistic License - Geography: Appears to be set close by San Francisco. However, many cities and towns are very fictional. The story mostly takes place in suburban "Blancoville," and NemoConTech is located in "Santa Marina," a fictionalized San Jose. The town of Sand City is real, though - it's just outside of Monterey.
Bilingual Bonus: Several in different languages. For example, Tim's new school, Ojo de Cielo High, meaning "Eye of Heaven" in Spanish. Episode 3 reveals the source of this name. Episode 6 reveals just how well said source deserved its name.
Disproportionate Retribution: Forms the backbone of Episode 3, where students and teachers are rude and abusive to the Green Club for daring to build a mini-windmill display on campus. The school superintendent even name-drops this trope when he criticizes the principal's poor handling of the situation.
Green Aesop: Zig-zagged in Episode 3. The Green Club is able to reveal that the builders of Ojo de Cielo High deliberately dried up the original springs so they could build on the site, and it's suggested that principal Matthew Cyrus is part of a conspiracy to cover it up. The real message, however, is that one should stand up for their constitutional rights, rather than a straight-up example of this trope.
Hypocritical Humor: Mr. Necker, Tara's English teacher, featured in Episode 3. He and a number of students have formed a Glee fan club, seemingly to promote tolerance, and yet he has no problem being insulting and abusive to those he doesn't like.
It Runs On Nonsenseoleum: Episode 6, to an extent. The author even lampshades it, claiming that writer's block made him desperate to finish the story, and suggests merely overlooking it as if it were part of a completely different universe than the regular story.
Ansem's ethereal blades are referred to by name in Episode 4, which is also named after Vexen's shield.
At one point, Axel says, "Got it memorized?"
Numerological Motif: Braig gets one with the number two. His last name is a combination of the Greek prefix and Spanish word for two, he's bi, he has one side of his face scarred, and he's second-in-command to Ansem, as company president.
Who Names Their Kid "Dude"?: When the Nemos adopt their twin sons, as shown in Episode 2, Ansem questions the logic behind the birth mother's request that one of the boys be named "Demyx." So he decides to call the boy "Timothy" instead.
You Keep Using That Word: In Episode 3, Mr. Necker attempts to justify his insults to Tara by saying it's a Comedy Central-style roast. Tim and others are quick to inform him that it's not a roast if it's not meant in good humor.