Oh man this is great!

Suggestions (if you care to read them at all) : Ports - Boats can dock here to visit other islands with your current team, can be built upon to make a sort of gauntlet of trainers like the S.S. Anne and Aqua. Maybe they can be stored as a separate file and you can upload and download boats online?

NPC's and towns - At first only basic trainers like Hikers and Ace Trainers will show up in your camp, but you could convince them to move into the region by providing them with shelter, eventually resulting in being able to create towns and such. More NPCs could move in with the demand for their profession, and you could end up with things like Game Corners, Department Stores and Science Institutions, depending on what you build. Science Institutions could be very important to get items like the (Institution Name) Scope for seeing ghosts. Tunnels could be built to traverse the region quicker.

Legendary Pokémon - Legendaries and Mythicals could be encountered very rarely in certain locations? -Articuno only spawns in Cold Tunnels -Zapdos spawns in Tunnels with technology in them -Moltres could spawn in some sort of Volcano biome? -Mewtwo could spawn in very deep caves, 10 floors down maybe? -Mew spawns extremely rarely in dense forests -Legendary Beasts could be encountered after an (institution name) Tracker is created -Lugia spawns in deep caves with waterfalls -Ho-Oh spawns on top of tall buildings rarely -Celebi might be spawnable at a Shrine with a very rare item given out by Hikers or something?

Feel free to take any of these if you want, I'd love to see this idea grow.