Johto had a war with Kanto and evidence below points to such
>Kanto decimated everything which is why Johto is so underdeveloped in terms of technology and areas like Blackthorn look ravaged
>And this explains why Kanto Pokemon are so prominent and the Johto ones are practically on the endangered species lists.
>The sage from Sprout tower says Pokemon are not tools of war, indicating that he's seen them be used for such.
>Ho-Oh going away because the people became violent and impure of heart of his presence.
>Celebi leaving Ilex forest as it was damaged in the war, Celebi only visits pure forests
And Thematically some pokemon are war related whether directly or indirectly
>Pineco: Grenade
>Forretress: A fortress
>Mantine: Fighter aircraft
>Remoraid: Gun
>Octillery: Tank and bazooka, signature move is Octazooka
>Pupitar: Kind of like a shell missile, dex entry from DPP says: By venting pressurized gas, it can launch itself like a rocket.
>Tyranitar: A Kaiju and godzilla-esque which are destructive monsters who engage in combat with military
>Skarmory: A metal plated bird, a bit of a stretch but it could be a fighter plane like Mantine, its counterpart.
>Donphan: An armored pokemon
>Steelix: An upgraded steel plated form of Onix, probably evolved to fight in wars
>Scizor: also upgraded from Scyther to fight better
>Noctowl, Sneasel, Ariados, Crobat all being adept night time scouters/predators
>Delibird: gives food to lost and hungry soldiers and pokemon. Present also explodes, probably to defend itself from enemies
>Ampharos: guides war ships and ships carrying rations in Olivine City

Johto being the first region with steel and darks, both typings being suitable in combat and related to war thematically. War is gruesome like the dark type and steel is used by the military for many things.