I'm interested in the idea, but not sure if I have time to help with it, or even join. I've one rp at the moment (assuming another one I'm in is dead...) and I am trying to keep it that way until things calm down, at least. I also haven't finished the game completely yet, so not sure how much of a help I could be. I can try though, but that would have to be a lot later.
I can give some fast advice/opinions right now, though?
1. For the region though, I'd suggest using an already existing one - either the one in conquest, or transforming one of the main game regions. That way, people have a basic grasp of the places and geography, and all you have to do is mention things that are different from canon (like earlier time period, what kind of people/Pokemon live there, who the shogun is, etc.)
2. When it comes to Legendary Pokemon, I'd say either omit them or have some really strong NPCs hold them, but not necessarily the players - unless everyone gets one. Otherwise things might get messy and 'wahhh he has one why don't I'-y.
Just my two, really quick cents.