Let's see...logically, Sinnoh would be allied with Almia if I'm correct about the geography. Johto would be allied with Kanto. Johto would have 251 Pokemon, Sinnoh would have 210, as well as some Ranger capture devices.
All in all, I'd fight Sinnoh.
WYR be trapped in Hoenn or Unova (if you could only use Pokemon introduced in that generation)?