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Well here is an interesting idea I have had for a while;
>Steelix
I've often said that Steelix most likely originate from Sinnoh, Iron Island. Steelix only evolve via the man-made Metal Coat, and yet for the first time, were found very commonly in the wild on Iron Island. Now technically speaking, Game Freak did eventually add them in two other locations in HG/SS (the Johto Post-Game in very rare numbers) and B2/W2 (a few mountainous areas in very rare numbers, post-game only) - However based on the dex entries suggesting the travel through very deep undergound tunnels, their rarity outside of Iron Island, and the fact that they only just showed up in Unova in recent (in-universe) years, I do truly think that Iron Island was supposed to be seen as their natural habitat, where they evolved naturally.
And I mean, the hint is in the name of the island.
>Rhyhorn
This is a simple one - This line is surprisingly uncommon in MOST regions. In Kanto, the line was only found in the Safari, man-made caves, or Cerulean Cave (basically a nature reserve from Mewtwo, further backed up in X/Y)
However Rhyhorns Dex entries claim that it lives in mountains and developed hide strong enough to protect it from lava. This is repeated in multiple dex entries, including that of Rhydon. The only region where Rhyhorn are found in mountains, including the Volcanic Stark Mountain, is Sinnoh. And while I don't usually treat the original implementation of evolution lines as concrete proof of a Pokémons habitat (I mean, obviously, these theories are entirely about cross-generational nativity and habitats), it is still worth mentioning that the line was "completed" in the Sinnoh games, so maybe that's simply where it best fits.
