I have two of my own:
1) Ash died in the 1st episode of the TV show.
Pikachu's attack seemed really strong, it made the Spearow leave, but Ash seemed OK. Ho-oh flew overhead, it could have brought him back. Admittedly, this probably isn't true. The writers probably chose Ho-oh because they wanted to reference the coming sequels, and Ho-oh looked better against the sky.
2) Your rival in the 1st gen games joined Team Rocket.
I was wondering why your rival appeared in Silph co. and the Pokemon Tower. If he was there before you, why is Team Rocket still there? Earlier in the game you were asked to join Team Rocket, and your rival is always one step ahead of you. Perhaps he got an invitation and accepted it. Admittedly, this is probably just bad writing; the earliest games didn't have a well-developed story.
As I said, these probably aren't true, but it's fun to think about.
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