As djonn said, it doesnt sound like an adventure as what pokemon is supposed to be...
so instead what if this war happened all in the background? like you would hear all these stories of this war but wouldn't pay much attention to it because you were out adventuring and having fun.
but slowly you'd be shown how this war is affecting peoples' lives, and halfway through the game you'd have to pick a side. of course you would still be going to new towns and stuff, but that decision you made also affected certain storyline elements. Like some towns hate you, some adore you, and even the gym leaders change aggressiveness towards you.
fast forward to pre-elite four. your all pissed off and stuff because all you wanted was to have a carefree life but the freaking continent is all mad at each other. not just that, it seems that the leaders of opposing sides got their legendaries too. you are a hero and a villian, using pokemon as weapons. you notice that and realize they're suffering and blah blah blah.
and so what happens now is you try to destroy both sides physically, because your an outcast now. your now a hero of the people and the pokemon, but not the legendaries. they are the god of war and the god of triumph, created from the imaginations of long ago.
now your fighting 2 people on each side who are the "elite four". you are sure enough to win now! but as sudden as your victory comes both armies team up to rid of you, the threat that is stopping them from conquering the land. so the last battle is obviously a forced double battle.
"but its not over yet" you hear. it seems a third legendary has heard of the great task you've placed on yourself,(and after his "you gotta prove to me your the stuff" speech), the god of peace joins your brigade. you battle and win with the pokemon and townspeople cheering you on. both armies eventually disappear and leave your land alone forever.
now its postgame. all the words of you being a hero quiet down. the legendaries runaway sans the god of peace. what he tells you to do now is help reform the towns and bring back all the people, pokemon, etc. so what you'll be doing postgame is just little story quests to help out a bit, (and bringing in some far-region pokemon!).
thats all I can think of for now :D