[@onenote] The overall story will be of the beginnings of a war started by religious zealots that wish to make Arceus worshiped world wide, along with a small "cult" of Rayquaza followers who emerge to combat the larger Arceus group. 
Naturally there will be plenty of character driven stories and plenty of side stories but the religious unrest will be the longest story line.

If attempting to challenge a Pokemon leauge is your goal that's totally fine, or just going on a journey in a more grounded Pokemon world. Joining a religious group would be an interesting turn too.