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>Gen 3
Kanto wins
>Gen 4+
Hoenn wins
In fact, I'd be willing to say that if you matched up every starter trio in a 3v3, Hoenn would come out on top most times simply due to Speed Boost Blaziken. The only matchup that is kind of hard is vs Kalos, because Ash Greninja is a huge danger, but even then, if you get Blaziken out on the field against Chesnaught, it's GG then and there.
Conversely, Gen 2 does the worst. Contrary Sceptile makes Gen 5, which would otherwise be last place, into the 3rd place threat, ahead of Kanto, behind Kalos.