Voice acting: Characters communicating through textboxes is extremely outdated. Future Pokémon games are definitely long overdue for voice acting. The Nintendo Switch and other future consoles for Pokémon games definitely have the power to allow their characters to speak. If Pokémon Masters Ex can do it, the mainline Pokémon games definitely can as well.
National Pokédex: Instead of only including certain Pokémon in a specific Pokémon game, I would include all Pokémon in the games, similar to the mainline Pokémon games that existed before Pokémon Sword and Shield. Therefore, players would no longer have to worry about their favorites not being included in the next generation of Pokémon titles.
Paired version removal: Pokémon truly does not require the release of paired versions to thrive as a video game series. Paired versions are essentially the same game, with only a few minor differences between the two. Instead of releasing paired versions for every new generation, I would instead only release a single Pokémon game with much more content and DLC.
Updated Game Corner: The original Game Corner with the casinos and its Voltorb Flip replacement were horrible. Instead, I would re-introduce the Game Corner, but make it a place where you can play minigames with your Pokémon similar to the minigames in the Pokémon Stadium series, which can be a fun way to bond with and interact with your Pokémon beyond battling. The player can earn coins when they win games and exchange their coins for fabulous prizes.
More robust competitive scene: When playing competitively in Pokémon, in ranked battles, players are practically limited to 4v4 Doubles and 3v3 Singles, with very limited ruling options. Instead, I would include more formats for ranked battles, similar to Pokémon Showdown, which would allow players to play competitively in several different ways. In unranked battles, I would also allow players the chance to fully customize the rules to their liking. For example, instead of setting pre-made rules such as flat 3v3 rules or rules with no legendaries, players should be able to customize them to "one legendary per team" and so on if they wish.
Increased difficulty: Face it, Pokémon is extremely easy. I would change the gameplay to make Pokémon more challenging. Trainers would have Pokémon with better IVs and EVs as the player progressed through the game, Pokémon Champions would have Pokémon with perfect IVs, maxed EVs in their best stats, and helpful Natures, much like real-life competitive players, and most trainers in the game would have Pokémon with held items.
NPC awareness: This might be a small change, but I want to showcase NPCs doing more than simply standing in one spot for the rest of their lives. I want more NPCs to at least have certain routines that they're programmed to do and interact with the environment to make it seem as if the Pokémon world wasn't made only to accommodate the player. For example, I want to see more trainers walking into Pokémon Centers, Pokémarts, and whatnot. In addition, I would have NPCs acknowledge certain Pokémon used in battle. For example, if I challenge a random route trainer with Arceus, I want him or her to say something like, "Wow, Arceus! How in the world did you get that?!" It would make the Pokémon world feel more alive.
Improved communication features: I would give players communicating online the option to voice chat, which would make playing competitively online with friends and/or using features such as the Union Circle much better.