another thing about the system we are trying to create: the plan is if your mods generations match (a 'generation' being a set of data for items and pokemon, which are too important to battles to not have everyone using the same data) you can take your character into coop games of that world. if your mod doesnt use a custom 'generation' it'd be compatible with the base game, so mods could allow you to start in a region, but you can visit others by cooping with people who are playing other 'versions' (thats what a mod will be called in this).
but ideally in the end the base game should probably have you start in johto, go to kanto, then from there you can go to sinnoh, hoenn, unova etc. but someone has to make these regions, lol. i know people are making hoenn, and we're making johto and kanto, so like i said, if the OP wants to do this, make a region no ones making and try and merge it later.