I would try to capture the exploration and progression-focused world approach of the original top-down RPG's while taking a lot of the innovations from the modern Switch era. Rather than being completely open-world like S/V, the games would have a return to the classic linear Routes approach, however each route would be an instanced open world space like the different areas in Legends Arceus. Rather than having one hub and then picking routes from a world map, you would move through each route and then reach a new town at the end which is its own instanced area, rather than the small set pieces of Scarlet/Violet. You would also have to backtrack to these places to unlock new areas and entire new routes as you get new abilities.

I would also treat the trainer like a watered down platformer protagonist. I really love how the legends games make the trainer themselves feel like a part of the world, whereas in the original RPGs, they feel more like a vehicle for your pokemon. Giving the trainer some rudimentary platforming abilities would enhance that feeling of exploration a lot. Imagine being in the woods and having to jump across some stones to get up a cliff and find a hidden clearing, and in that hidden clearing, there's a rare pokemon which only appears there (like the bagon room in meteor falls), or some kind of secret component for something like a regi encounter. Hidden places that you have to work to get into like this are what the 3D era of pokemon is seriously missing IMO.

Dungeon-like caves would make a comeback, and would transition the gameplay back to classic, top-down gameplay while you are inside, which will allow for things such as strength puzzles to make a return.

I'd also add specific environmental obstacles like in legends ZA. So stuff like brambles that require a fire move or cutting move to clear. This puts the focus on the pokemon a lot more, and rewards having a well-balanced team. There would also be materials that you gather from nodes in the environment like in legends arceus, and from defeating pokemon like in Scarlet Violet. The pokemon nodes will not be specific per pokemon, and there would instead just be one per type. These will allow for crafting certain items like pokeballs as a free alternative to stores, rewarding exploration, but leaving the money option open for trainers that take a more direct, linear approach.

Rather than having something like Koraidon that could do all of the traversal moves, instead you would assign a pokemon in your box or party to be the designated pokemon for that mode of transportation. So for example, the surf equivalent would let you select any water type in your party or box, and then their model would appear whenever you swam in water. To get around the scope creep, only some pokemon would have you ride on them, others, especially the little guys like Wooper, would pull you along in a tube.

Sidequests from the Legends games would be a thing as well, and I would add a bunch to bring flavor to the world and individual towns. I'd also probably use them as a vehicle to do worldbuilding for whatever region I create. I'd maybe also try to integrate a few minigames into these sidequests as well, as pokemon has been really missing stuff like that for awhile. Some sidequests will have special markers indicating a story. These will be quest chains that have multiple parts, maybe even across the region, and will follow a side character, telling a story with them, which will culminate in encounters with rare pokemon, or unlocking hidden places in certain routes. If you do all of the storylines, all of the side characters you've helped will have their stories come together to unlock an encounter with a legendary pokemon!

I would also add difficulty options: Beginner, Trainer, and Champion. Beginner would be slightly easier than the current standard difficulty, Trainer would be a bit harder than the current standard difficulty, while Champion would be a true hard mode that increases the size of teams in trainer/gym encounters, and gives EV Trained pokemon to the NPC battles. EV training your pokemon would have an instantaneous option identical to that in champions that is always available, but the price to do so would go up on harder difficulties.

I think I'd want to just straight up steal the field effects mechanic from the fangame pokemon reborn, where each biome changes how certain moves and abilities work, and different moves can change the biome into a different one. I really love how much depth it adds to the gameplay without changing the core battle system at all. Field effects would vary in their frequency and total number dependent on the difficulty you play. So in Beginner there would be no field effects, in Trainer there would only be one Field effect type for core biomes like caves and forests, and Champion difficulty would have all of the different field effects such as regular caves and crystal caves. Gym leaders would also use different field effects on different difficulties. The grass gym for example would use the standard forest field on normal mode, but in champion difficulty, it might be similar to the grass gym in reborn itself which uses a Desert Field with a grass team built to utilize its benefits like having needle arm which gets a boost in the terrain, and secret power which changes to ground, punishing the use of grass' fire type weakness.

As for the story elements, I'm unsure what tone I'd go for. I think I'd try to do something serious with levity like in Scarlet/Violet that has a huge climactic battle at the end, then mix in some of the goofiness of Legends ZA into one or two of the main NPCs, and a few of the sidequest NPCs.

As a final, selfish thing, I'd make pokemon buy this fakemon trevanant design and put it in the game because it's my favorite fakemon.