Ascended Fanon: The producers of this film openly admitted that they turned Cloud from the serious hero into the brooding loner because the fans would be familiar with this image of him.
Casting Gag: The voice actress for Marlene in both Japanese and English (Sumire Morohoshi and Ariel Winter, respectively) shares the voice for characters in other Square Enix works: Mog and young Kairi, who are also cute, small characters. Andrea Bowen, who played the Moogle Girl, was also upgraded to voicing Aerith in Crisis Core.
Development Hell: The original movie was announced at Tokyo Games Show 2003, and wasn't released in Japan until late 2005, due to significant changes to the script during early development. Complete was announced at TGS 2006, and would subsequently not be released until March 2009.
Dueling Works: With The Legend of Zelda: Twilight Princess, as a continuation of the rivalry between their predecessors, with both works taking on a more "realistic" aesthetic and giving their respective protagonists (Cloud and Link) a wolf motif. Both works were successful commercially, but Twilight Princess was met with universal acclaim and continued to be quite well-regarded over the years (if not to Sacred Cow levels like The Legend of Zelda: Ocarina of Time), whereas Advent Children was very divisive (granted, its format didn't do it very many favors).
Fan Nickname: SHM—Silver Haired Men for Kadaj's gang. They were called this for a long time before the official release of their names.
No Export for You: Complete's vocal theme, "Safe and Sound," is not in Western releases of the film, which is odd considering that the song is written by Gerard Way from My Chemical Romance and sung entirely in English. Furthermore, it's only available on the Japanese iTunes. "Calling" from the original version was used for the Western release.
The Other Darrin: George Newbern took over for Lance Bass as Sephiroth starting with this movie. For the Complete version, Aarom Refvem and Ariel Winter replaced Benjamin Bryan and Grace Rolek's Denzel and Marlene since the latter two actors grew up and couldn't voice them for the new scenes. Mandy Moore had also voiced Aerith in the first Kingdom Hearts game but was replaced by Mena Suvari for this one.
Recast As Regular: Andrea Bowen, who voiced the Moogle Girl, would later be upgraded to Aerith's regular voice actress. She has voiced the character in three Final Fantasy projects since.
Throw It In!: Several minor aspects of the film, such as Rude's extra sunglasses, were tossed out by development staff as random ideas not in the original concepts, and got approval.
The initial choice for Denzel's Japanese voice actor was Koki Uchiyama. However, he was a bit too old to fit the bill, but Nomura later used him in Kingdom Hearts II as the voice of Roxas and later in Kingdom Hearts: Birth by Sleep as Ventus.
At a very early stage in development, the only featured characters were going to be Cloud, Tifa, Kadaj and Sephiroth. The run-time was also planned to be far lower than in the final movie; early interviews mentioned around the 40 minute mark. This would change as it became apparent that fans were expecting much more than the initial script apparently had, prompting a fairly extensive rewrite. The TGS 2003 trailer, and the unused footage it contains, probably comprises the remains of that early version of the movie.
Word of God says Cloud's new Limit Break was named "Omnislash Version 5" because it was the fifth version they had come up with. One wonders what the unseen others looked like...