Each version/region would have different Pokemon, trainers, and gym leaders, but there would only be one evil team spreading their influence across both regions simultaneously. You would hear about the evil team's exploits in the other region, but only experience what happens in your version's region. And of course, their plans and/or ways of going about them might change slightly based on your version.
Both versions would share the same Elite 4; the regions would be connected like Johto and Kanto. After beating the Elite 4, you could go to the other region and earn that region's badges. The wild Pokemon and trainers would be stronger in your version's non-native region; basically, it'd be like Gold and Silver, if Gold went Johto -> Kanto and Silver went Kanto -> Johto. --- U say U want a Revolution Well, U know Wii all want to change the world
I was thinking more like The Legend of Zelda: Oracle of Seasons/Ages. Heck, maybe one region could be overworld puzzle-based with normal computer AI, while the other region could have a simpler overworld but with tougher AI, similar to how Ages was puzzle-based and Seasons was combat-based. --- U say U want a Revolution Well, U know Wii all want to change the world