>>46196702I'd basically remake the entire thing from scratch.
The gen1 story only works because of the huge amounts of minimalism the games were forced to have. Once you have to translate it into a story that takes place in a world where a town has to be a town and not two single room houses and a pokemon center things like a rookie trainer defeating a powerful regional criminal organization stop making sense.
I think Festival of Champions did a good job of showing the scale of the Team Rocket plotline but it still put an arm's length between it and its plot because it's kind of stupid. Green's legendary meme Raticate dies to one Koffing using poison gas after raiding a tiny poaching operation. The idea that Team Rocket would vanish after Giovanni is defeated, not arrested, in Silph Co. is pretty absurd.
Also, what would be the point? Its whole purpose was to shill Charizard© from Kanto®'s Mega Form™. Origins was never meant to be a story.