No, there is some logic behind some of them. For example Absol are sometimes placed on routes where disaster is about to strike as a reference to being harbingers of disaster.
But yeah, a few times I have found myself asking why some Pokemon are where they are. Maybe instead of a new thread
JES could ask to combine it with the Move Oddities thread?
I suppose I could, but I also wanted to list what regions each Pokémon is native to, because I find the subject interesting, specifically in the order of the Pokédex, doing one or two evo lines every couple of days. I find it fascinating that Riolu and Zoroark can only be found in Kalos, while Zorua only lives in a very small population in Hoenn, while we have more common Pokémon living in some regions, but not others.
Another standard example is Pidgey:
They live mostly in Kanto, Johto, and Kalos. But a small-medium sized population also lives on a specific route in Sinnoh, while some also live specifically in the White Forest in Unova.
Pidgeotto live in less locations and are less common, but too can be found in Kanto and Johto, but are non-existent in Kalos. Forget about the other regions.
And Pidgeot are so rare that you can't find them at all.
I find that interesting, and there I think are things that we can infer from this type of information such as that Pidgeotto rarely evolve in the wild, for perhaps a number of different reasons, most likely dying before attaining the level necessary to evolve, which could also be for a small variety of reasons, such as moving to another unexplored region upon evolving or to remote, inaccessible areas.
And I agree with Pikachu, in that the Friend Safari is not likely the native habitat of the first and 6th generation Starters, though I still suspect that there must be wild populations, and we just haven't been able to visit the region that they come from. I don't think they are an artificial species selectively bred specifically to be given out to trainers. I mean, look at Charmeleon to Charizard for example. If I were selectively breeding a species to be handed out to kids, I'd want to breed out the aggressive tendencies.
But I already see one naysayer who thinks that such a topic would be a waste of a thread, so I'll let others put their input into whether they'd find such an analysis of interest before deciding what I'm going to do. If the popular opinion indicates such a thread would be unpopular enough to likely be closed by the moderators, maybe I'll just do the really interesting examples in the Movepool Oddities thread.