The Kaiba in the movie is Cyber Kaiba from the manga novelization.It would explain Kaiba's memory discrepancies between the series and the movie, how he was awake after the Mind Crush, his hair/eye color changing, and how he seemed to grow taller.
Aileen Rao was brainwashed to work for Kaiba at Death-T.She only gets a handful of lines and none of her previous characterization was delved into, and the Toei anime is weird enough that something like that could be possible.
If the series had continued to Duelist Kingdom, Pegasus would have had blond hair.Mainly for the series' habit of giving characters different hair colors as well as a color palette from Yu-Gi-Oh! Monster Capsule GB depicting him as such.
If the series had continued to Duelist Kingdom, Count Sheldon would have replaced the ventriloquist from the manga.He already displayed a proficiency for dolls as well as life-size puppets, and could change and throw his voice flawlessly, so it's not too much of a stretch to think they'd reuse him.
Risa and her sisters would have met and/or teamed up with Yami Bakura.They have a shared interest in magic, are good at Duel Monsters, and stole or want to steal the Millennium Puzzle.
The series takes place in the same continuity as Sailor Moon.A woman in the water park episode has an uncanny resemblance and posture to Sailor Neptune, and Yugi is essentially a Magical Girl in the same manner as Usagi and her friends.