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This is actually a fun idea. I think I could keep fucking around with it for a while.
Stories would be told slightly non-linearly.
Gen 1: Team Rocket would be fought in Silph Co. and *then* Celadon. That's where the Trainer gets Porygon, but it's slightly glitchy and they don't understand how to control it, so it gets boxed before league.
Sandshrew
Ends up getting a Leaf Stone from Celadon instead of a Fire Stone, so Growlithe is traded for a Dodrio. Leaf Stone is used on an Exeggcute they happen to have.
Gen 2: Ampharos is quickly KOed against Gyarados and the rest of team is pretty useless. A Steelix shows up to defeat Gyarados and that is caught instead. As well, Up-Grade is attained and that lets Porygon evolve and become usable.
Gen 3: Trainer gets 2 starters.
Gen 4: Male Combee is a running gag throughout the series until a beekeeper trades them a Shelgon (which is impervious to Vesipquen stings) for it.
Gen 5: Doesn't meet prof in the region. Swampert is traded for a Cottonee. Old ace Nidoking is used by trainer throughout the region to compensate for lack of a good starter. Torchic is finally properly trained up and willing to evolve.
Lickilicky is accidentally confused with a Ditto impersonating it and gets mixed up (accidental trade)
Gen 6: Gets given Eevee as a starter. Accidentally evolves it into a Glaceon instead of a Sylveon after confusing an Ice Stone for a Moon Stone (Ice Stone isn't actually consumed, Moon Stone wouldn't have worked anyways)
Gen 7: Sandshrew gets traded for a Vulpix which promptly reacts with the unused Ice Stone from Gen 6.
Litten swallows an Everstone lol