Brains: Evil; Brawn: Good: Averted. The good guys rely just as much on quick wits and critical thinking as the bad guys, if not more so.
Break the Cutie: Sayaka gets hit with this a lot harder than in canon. Not only does Hitomi snatch Kyosuke, but she then gets a No-Holds-Barred Beatdown by Sho Minamimoto, and THEN she gets kidnapped by a bunch of monsters after trying to rescue Milly.
The Black Knights know about Zeta Beams; Zero travels to his base via one, and Kallen notes that the Guren's claw can shoot any kind of radiation, including Zeta Beams.
The Avalon that Morgaine tried to steal turned out to be fake because the real one is inside Shirou.
Continuity Snarl: A version of the Kingdom Hearts mythos exists in this setting, but it's almost unrecognizable from canon. For starters, instead of Donald and Goofy, this world's Sora apparently teamed up G'nort and Klarion the Witch Boy.
One Steve Limit: Aside from the aforementioned "Hope" issue, Gendo Ikari and Detective Ikari aren't the same person. But they are brothers-in-law; Detective Ikari is Yui Ikari's brother, making him Shinji's uncle.
Morgaine Le Fey brings Mordred along with her, like in Justice League, but Mordred is completely different.
Astute readers might notice that Hope is a Fullmetal Alchemist-style Homunculus who has severely-weakened versions of the powers of seven other homunculi, including the manga version of Pride and the 2003 anime version of Sloth.
Translation Conventions: Everyone is assumed to be speaking Japanese translated into English unless stated otherwise. One of the authors notes explains that Edrobot didn't refer to a police station as a Koban because few Americans know what that word means.
Token Evil Teammate: Not in the story itself, but one Channel 52 segment implies that Vriska Serket is a member of the Teen Titans, so presumably she's one of these.
Took a Level in Kindness: Gendo Ikari is a hell of a lot nicer than he is in canon, treating his son with a surprising amount of respect, and even going so far as to secure the funding for The Team to form in the first place! But he's still planning Instrumentality.
World War II: Downplayed, at least compared to the JSA. The team was originally conceived in the aftermath of WWII as a way of getting around Japan's ban on armed forces, though the team was never actually created.