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Probably Johto, I feel like in terms of a region worth exploring from the anime's standpoint where the focus can be put on non-badge related tasks it probably would do the best thanks to being more rural than most (bar Sinnoh) and having that untapped history with Alph.
As for team I went with mostly Johto'mons although in some cases the Pokemon starts out as a Gen I or becomes a Gen I Pokemon, all of them are Pokemon I strongly like with Houndoom being my no.1 overall, although I don't think Houndoom or even Houndour would make for a good shoulder'mon but could serve the powerhouse role, Misdreavus meanwhile would fit the shoulder'mon role much better. Ledian would be that early catch akin to most regional birds for Ash. Eevee would be the late bloomer so to speak, y'know one of those Pokemon that stays in its base form for most of the adventure. Kingdra would be a bit of an oddball, because the Horsea line is pretty unusual compared to what most protagonists in the anime have (aside from Misty's Goldeen & Starmie) I figure it'd be a Pokemon that would basically be as much about raising it as well as actually understanding its needs (beyond access to water obviously). Clefable would be the egg'mon given this is Johto after all, probably wouldn't evolve into Clefable though until pretty late like around Blackthorn due to the availability of Moon Stones.
As for companions, I'd think Whitney would fit pretty well given her whole thing of being a sort of rookie trainer with hidden strength. Eusine meanwhile obviously would be more significant for the Alph stuff as well as legendary beasts and tower duo, basically giving the incentive for the trio with different reasons to travel the region. Plus you'd get some interesting situations like Goldenrod where Whitney would probably be well aware of Misdreavus' immunity to Normal-Types and so would have a secret weapon Pokemon to counter it.
