For starters, let go of Game Freak's engine and possibly use UE4 to streamline development. This would probably require some time to rework all of Pokémon's systems into the engine, but it would most likely pay off in the long run.
A large region with a variety of biomes. The game would include about 500-600 native to the region, 120 of them would be tied to seasons that are tied to the real world region the player chose when first launching the game. 30 for each season. Game would also have a weather system that would change the spawn rate of certain species in certain weathers. The game is mostly open world with a few closed areas where necessary, like the dungeons. All Pokémon are available via Home transfer.
Make it a live service game with new post-game content delivered via post-launch updates. Make the entire game playable in co-op with friends. Party system with up to three players can take on trainers, gyms, league and dungeons that will have teams/encounters adjusted to the party size and team levels. Plenty of puzzles in dungeon areas like caves and dark forests, puzzles also adjust to the number of party members to incentivize team work (like Lara Croft & The Temple of Osiris). Only a few of the dungeons will in the player's path during the main game, the rest of it will be optional and more challenging, part of side-quests and will also inhabit rare pokémon and reward the player with better items.
Difficulty levels. Harder difficulty levels disable auto Exp. Sharing (and it becomes an item you obtain towards the end of the game), increase overall NPC team levels/IVs/EVs, disable PC access from anywhere in the region and introduce NPCs with actual strategies.
Battle system is the same, with small improvements to make it more snappy to avoid dragging on.
A new form of base/camp; you can select one of the variety of camp areas in the region to set up your base. There you can build your tent/house and have your friends visit in real time. You can customize the place to your heart's desire, with a variety of furniture and useful tools, like an IV checker, incubators where you can set up to 20 Pokémon eggs to incubate, training gear for EV training and a playground where you can leave two of your Pokémon bonding. Up to six Pokémon from your PC box will be randomly chosen to roam the base when you're visiting.
Post-launch content will include timed events like raids for special Pokémon, increased chance of IVs and shiny pokémon, etc., as well as full-blown expansions included in the Expansion Pass, with a new story, new areas and actual brand new Pokémon. New Pokémon will be patched into the main game so players can trade them if they don't have the expansion.
Monetization to fund constant post-launch support would be done in the form of cosmetic accessories for the trainer and the Pokémon as well as new furniture for your base, all of which can be acquired in in-game events but can also be purchased with real money.
Probably a lot of other ideas. This would most definitely not be possible in less than 4 years of dev time, though.