Well, since I’ve never actually played Pokémon Conquest it’s probably wisest to take anything I have to say on the subject with a grain of salt (or perhaps a whole shaker). Having said that, I think the presence of Mewtwo in that game (along with various other legendary Pokémon whose roles in the game conflict with their roles elsewhere in the franchise) makes it difficult to interpret the story as being historical in a straightforward sense – that is, I don’t think we’re supposed to imagine that these events literally happened in the past of either the main series of games or the anime. More to the point, I’m given to understand that the game offers multiple ‘campaigns’ or storylines, which don’t necessarily fit together in any coherent fashion, so it doesn’t even have its own ‘canon,’ really. I do think you can reasonably interpret it as “this is more or less what Pokémon training in a feudal setting would have been like.” The specific events are basically ahistorical, but the world and the society in which they take place – with their feuding warlords and mighty warriors who fight alongside their Pokémon – are not. If that makes sense.
Alternatively you could take it as, like, a bizarre post-apocalyptic future with civilisation being slowly rebuilt along feudal lines. Or something.
Pokémaniacal 