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I'd create a free-to-play title that contains all of the regions... but that you only get access to one region for free, before needing to pay for tickets to the other regions.

Each region would have its local pokemon, plus some pokemon that are cross-regional. There would also be locations in each region that would require things only obtainable in one or more other regions to access, so that additional bonuses come from buying more of the region-access tickets.

Each region would also have a storyline that must be completed before pokemon from outside of the region can be transferred in, kind of like how you need to get the Ruby and Sapphire in the Sevii Islands before you can trade between FR/LG and R/S/E. In this way, each region would act somewhat like its own new game.

There would also be some cross-region storylines.

Each region would also have its own level-up moves for pokemon, its own evolutionary paths (for example, only a few regions would have a Mossy Rock to evolve Eevee to Leafeon), its own TMs, etc, meaning that you need to buy them all to get all of the features, have access to all possible moves for each pokemon, etc.

Then there would be ongoing support in the form of new areas, etc, that would be available, sometimes as expansions to existing regions (for free to those who already have access to the region in question, thereby "sweetening the pot" for those considering buying the ticket to the region), sometimes as a "free to everyone" time-limited location (often as a form of advertising), and sometimes as an area or microregion you have to pay for a ticket to access (generally not time-limited).

I would expand the idea of Alolan forms to have forms specific to each region, including forms that aren't inherently native (you need to breed in the right way to get the local variation), to further expand the idea of increased benefit of having access to multiple regions.

I mentioned time-limited locations. They could also include "dream zones" with pokemon that can't be transferred out of the zone, and often break the normal rules. For example, one region might be a Mario Dream Zone, with Mario enemies replacing pokemon, etc. Such areas would be open for third-party content as well, allowing them to act as a form of advertising for other titles, too. In other situations, the dream zones might introduce new pokemon that will become available in a future region (like how Bonsly and Munchlax appeared in Pokemon XD), test out new feature ideas, types, etc. Or they may just change up the normal Pokemon conventions, as a way to maintain interest in the game.

But at its core, this title would play much like existing Pokemon games.

....

Then I would have another Pokemon title, operating independently of the above, that acts as an MMO, using a subscription system. It would have a time-dependent system rather than pure turn-based, and wouldn't have the classic regions - instead, it would have a new, super-sized region with some elements of random dungeon generation to keep things interesting.

It would break a lot of the existing Pokemon game rules, in order to freshen up the franchise. "Catching em all" would be made significantly more difficult, because perhaps some pokemon aren't in unlimited supply in the way they they basically are in normal pokemon (in the sense that anybody can get one) - so for example, there may only be a few thousand Mew in the entire world, rather than each person being capable of getting one, and completing your pokedex would require you to do all sorts of extra trades, etc.


Anyway, that's what I'd do with it.