Pokémon Conquest/WMG

Mitsuhide will be the True Final Boss

According to history, Mitsuhide betrayed Nobunaga and attacked him at Nijo Castle, forcing him to commit Seppuku. Then, according to The Other Wiki, "Just eleven days after the coup at Honnō-ji, Mitsuhide was killed at the Battle of Yamazaki and his army was defeated by Hashiba Hideyoshi, who eventually became heir to Nobunaga's legacy. He is more widely known as Toyotomi Hideyoshi." Given most trailers seem to imply Hideyoshi will be on the player's side, it makes sense to re-enact these events. (minus the seppuku of course, but then again, you never know) My guess is that Nobunaga will be the Disk One Final Boss, (or possibly even The Unfought) after which Mitsuhide will become The Starscream, hijack the plot and become the primary antagonist from then on.

This series will still be in the same timeline as around Pokemon RBY or RSE

Or, at least, it is not set in the past. Otherwise, how do you explain Mewtwo?

A Celebi or Dialga did it?
Or perhaps Rule of Cool?
Maybe it's set in the present... on a continant stuck in Medieval Stasis.

This game takes place in the distant future of the games.

I say this because, as far as we know, the regions in Pokepan don't seem to be united.