Pokémon Open World Concept

I think a case can be made for Pokemon being open world, here's my pitch:

The only way I could see Pokémon being open world is by making the gym challenge optional, implementing skill trees, but instead of skills it's Pokémon moves, and some of those moves have out of battle effects that allow you to explore the rest of the world, like surf allows you to travel across the sea and find Pokémon in the world, acquiring the dive skill allows you to dive underwater with your Pokémon and find deep sea Pokémon, and so on.

Having trackable side quests is possible, simply make the evil team HQs exist within the overworld, capturing these HQs reveals collectibles like Pokédex pages, pseudo dens, and legendary nests.

For battles, you can customize your Pokémon and their Moveset with their full move pool to suit the battle you're in, and awarding a base amount of exp for winning, and giving you extra amounts based on how well you did, like clearing a battle without losing a Pokémon, or without getting hit, or even clearing it with fewer turns or not using certain things like mega stones or z-moves. Mega stones and z-crystals could also be another collectable revealed on the map through taking down evil team HQs, it would also reveal optional gyms, aside from the main 8 gyms dotted around the world.

Also, crafting pokeballs by finding crafting materials in the world, since open world games love that.

Just look at how games handle open world IPs and you have your answer of what an open world Pokémon game looks like, similar stat progression to fall out, skill trees similar to watchdogs and far cry 4, etc.

To continue, I think making the Gym Challenge a side quest instead of shoehorning it into the main story is a good idea.

There'd be 18 gyms, and each gym would reveal a set of collectibles that the player can use in battle, such as Mega Stones, and Z-Crystals. Each gym would reveal a set of mega stones for a Pokémon type based on the gym you completed, and would reveal the location of a single Z-Crystal per type.

In order to find the location of a gym, you would have to first remove the evil team influence in that region, by taking control of the team's watchtowers they've stormed that were previously used for Pokémon nature watches.

Doing so reveals small towns, locations of Pokémon groups (such as a group of houndour), and the locations of Pokeball factories and storehouses that have been taken over by the evil team of that region. In these PokeFactory raids, you must find the card key holder and battle them to win the card key and gain access to the main storeroom. Doing so will give you crafting materials for pokeballs, and money, you're also rewarded with Pokémon Stat Modifiers to amplify your moves in battle.

The difference between factories and storehouses is slight, but yields vastly different rewards. Raiding PokeFactories gives you the materials for making pokeballs, and Storehouses give you the pokeballs themselves. However there are fewer Storehouses and they're on a larger cool down to when you can raid them next, 48 hours real time, contrary to the 24 hours real time that occurs when you raid pokefactories.

Each region of the world map would contain a number of cities and towns within large overworld. Flying Pokémon will only allow you to fast travel to locations you've already visited, but to get around the world map at a faster pace than walking, I would think vehicles such as cars, bikes, and various other modes of transport would be crucial to this, however, vehicles in the Pokémon World are few and far between. This is where large scale crafting would come into it. You could use crafting components to make pokeballs, or you could instead, save large quantities of materials, like mechanisms, and take it to a crafting showroom, and make an engine. Different vehicles need different parts, and those different parts will need large quantities of materials, like metal, fuel, rubber (for tires), textiles (for seats), and glass (for windows). Now, you can find them in the world yourself, but you could also send out Pokémon you're not using on gathering quests to find these materials for you, however, these Pokémon you send out will be unavailable for selection until they return, they also have a cool down for use, similar to the PokeFactories and Storehouses, of roughly 24-48 hours depending on the vehicle and the materials requested.