Could've sworn I posted this back when RBY were released on the 3DS VC, but I guess not. Anyway, here's some food for thought.
We all consider Mr. Mime, Farfetch'd, Jynx, and Lickitung as Kanto-native species and part of the original 151 Pokemon. However, is that an accurate assumption? Those who've played Red/Blue know these four share something in common: they're not available in the wild in Kanto; there is only 1 of said species available in the game, and you have to trade for them with NPCs. Fast-forward to Gen II, and we see habitats in Johto containing Farfetch'd, Jynx, and Lickitung. This strongly suggests that these Pokemon are, in fact, Johto-native species, and that their OTs caught or imported them over from Johto, yet they still have data as known Kanto species in the first generation Pokedex.
Naturally, there are a few holes in this theory. First one involves Mr. Mime, which isn't available in the wild in Johto either, but became available in the wild in Kanto when Gen II rolled around. Also if you include Yellow into the equation (I don't really consider it a sister game as much as a game that was meant to pay homage to the anime), Lickitung and Farfetch'd have habitats in Kanto in that game, but still not Jynx.
There aren't any other cases like this in the newer games; it's just these one-off R/B trades. Was it simply a gimmick to promote trading with the NPCs (and the species were just made available in the wild later in Yellow & Gen II)? Or was it intentional foreshadowing to Gen II, since it's common knowledge that Game Freak was well underway in development for Gen II around the time that RGBY were released? The world may never know.
A possible Watsonian explanation for Mr. Mime is that the species isn't Johto-native
or Kanto-native, but is instead from Sinnoh or Kalos, as those are the only two known regions where Mime Jr., Mr. Mime's pre-evolved form, are found in the wild (although there are also Mr. Mime swarms found in Unova in White 2). In fact, my money's on Sinnoh, as the Pokewalker route Sinnoh Fields has catchable Mime Jr. there as well.
But what about the wild Mr. Mime found in Gen II Kanto? Perhaps some Mr. Mime were released into the wild after the events of R/B/Y, leading to the eventual development of a new population by the time Gen II rolled around. But then if Mr. Mime is actually from Sinnoh, why is it listed in the Kanto Pokedex? In fact, why are any of these four Pokemon in question listed there?
This leads me to a wildly new theory that contradicts my original one explained only two paragraphs ago, but I think it may be the more interesting one. All four species (Mr. Mime, Farfetch'd, Jynx, and Lickitung)
formerly had indigenous populations in Kanto. Migrations and trade led to the development of other populations in Johto, Sinnoh, Unova, and Kalos. However, for various reasons, the Kanto populations were either driven out or driven extinct sometime before Gen I (I would guess long before given that by Gen I the world at large has the "Pokemon are our friends" attitude). This is supported by the example of Farfetch'd, who were hunted to near extinction to be made into fancy meals. The Pokemon are still listed in the Kanto regional Dex because, despite having gone extinct locally, they were originally from that region.
Meanwhile, as the Kanto populations declined and disappeared, the other regional populations remained, enabling the trainers in R/B/Y to trade you the Mr. Mime, Farfetch'd, Jynx, or Lickitung that they caught from another region's local population.
Eventually, re-introduction programs were started. Some Mr. Mime from Kalos, Unova, and Sinnoh volunteered for the project and were brought over to Kanto after the events of R/B/Y, and by Gen II a sizeable population has developed. Presumably, the same project will eventually be carried out for Farfetch'd, Jynx, and Lickitung until they become less rare.
tl;dr: The odd population distributions are the result of re-introduction programs following post-extinction of regional populations.
