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I think I'd want a deeper re-working of the games.
Levels and stats would be reduced in significance, other than learning new moves and evolution, so that lower level pokemon won't be so easily 1HKO by higher level pokemon.
Moves would still have types, and be either physical or special, close combat or ranged combat in damages. Yes, that is right, damages, a move could have multiple damage types, for instance, fire punch would be half-physical, half-fire. Some superfluous types would be eliminated move wise, like dark, fighting, flying, rock and steel, those would all be 'pure physical attacks', for the most part, other attacks might be things like 'wind', 'sonic', 'fire', 'heat', 'telekinesis', 'telepathy', 'magic', 'water', 'electric' and so on, things that actually make sense for doing different types of damages. Pure physical moves would be split up like D&D into piercing, slashing, and bludgeoning.
Pokemon, rather than having types, would have 'attack affinities', attack affinities would be things like, 'claws n' (n is a number) meaning they have claws, so can use moves that require claws, and get a 'n' boost for the slashing or piercing portion of that attack's damage that, or 'ice n', and they get 'n' boost for ice damage portion of attacks, and can learn ice attacks. They'd also have damage levels, for instance they could have 'bludgeon def n' which if it was low, they'd take more damage from bludgeon damage portions of attacks, and if it was high, they'd take less damage from bludgeoning portions of attacks, and if it is 0, they are 1HKO by that type of damage, and if it is 100, they'd be immune to that type of damage, for instance 'ghost' pokemon would be immune to bludgeoning, piercing, and slashing damage, regardless of if it is ranged or close, but still vulnerable to stuff like telekinesis, fire, and electric damage, and that immunity would display itself as 100 percents on those def stats for that type of attack damage. This would have a range for each pokemon that is leveled up by training, within a small range.
Pokemon would have a limited number of attacks still, because it is feasible that it would be weird to train them to understand all sorts of different commands when they don't speak human language or truly understand it (for the most part, I'm sure a few do at least understand it, like some of the smarter psychic types), but instead of forgetting moves, they could still use old moves they used to know on their own initiative, and you could change up their movesets with a bit of training to remember old moves instead, and some smarter pokemon might even have moves that switch them between multiple movesets.
The battles would be 3D, and would operate similar to a blend of Tales of Symphonia and Digimon World. You can set a pokemon's attacks to different keys, and pressing those keys causes your character to command them to use that attack, so long as they're obedient (i.e. you caught them, and are treating them well, or you have enough badges), they'd use that attack next if they have the energy for it and they aren't distracted or interrupted and have the energy for it, and keep trying to use it until you let them attack freely, or do something else. The pokemon could also be commanded to do things like 'guard', or 'dodge', and some pokemon would get upgrades to 'guard' and 'dodge' like doing them on auto from special abilities or training, or from certain techniques, or might get special enhancements to them, like a pokemon that is taught doubble team, when told to dodge, would start leaving afterimages and moving around really fast as they dodge attacks. The pokemon would fight based on AI, moving around on their own and stuff, other than when you give them commands, and if you want to, you can just let them fight freely on their own, but most of them have dumber AI's, so they can be kind of stupid when let to do that.
However, there are exceptions to when they don't use AI's, like the character you control in Tales of Symphonia, you can sometimes take direct control of the pokemon, this involves certain pokemon abilities, particularly some psychic type pokemon, or if you play a psychic trainer with the skills to create a mental link to control the pokemon (which would either involve special training for your character and/or an option during character creation at the start of the game). Controlling your pokemon directly would have benefits of course, but would also come at the cost of your character being pained by the damage your pokemon takes, so you risk being knocked out when the pokemon is, even if you have more pokemon, and wouldn't be allowed in certain types of battles, plus some pokemon abilities and moves might be able to block it.
Pokemon would be able to learn some, in terms of their AI, for instance they might figure out that they can't physically attack ghost types, although this 'learning' can be turned into a disadvantage, for instance if one pokemon creates an illusion that they are a ghost type, or perhaps scares them into a defensive with damage types they are vulnerable to, some conditions like confusion would be connected to the AI behavior. You'd also be able to do things like cheer a pokemon on to raise their motivation, or help wake them up quicker from sleep, with some button mashing of a 'cheer' button, and there is sometimes cheers from bystanders or audience, and cheering at the right or wrong times can cause a pokemon to get boosted attacks or get distracted and mess up an attack.
Fighting types would be able to take advantage of attack combos and learning fighting attack combos at dojos, in order to combo close up attacks. Dark types would specialize in dirty tricks and being sneaky and if they pull it off, dealing 'sneak attack' type damage bonuses or 'critical area' type damage bonuses by attacking weak spots and such.
Leveling and training would involve a general level related to a pokemon's battle experience and AI level, as well as individual levels that are leveled up by specific training or other stuff like that, for instance they might have a 'fist attack level', with a certain range, and they can be leveled up to a degree in that, until they reach the max area of that range, and it grows the more they practice fist attacks in battle or do special fist attack training, such as learning punching techniques and punching punching bags in a dojo, or working out their arms in a gym, or a more temporary boost by putting on special glove equipment.
Pokemon would also have movement speed, and attack speed. Attack speed would be related to the levels they are in the attack stats for that attack's type and the individual speed range of that attack, while movement speed is how fast they move around on the screen in order to maneuver and avoid attacks or chase down their opponents, and some charging attacks would be aided by movement speed. So higher level in an attack makes that attack both more powerful and faster, and useable more often because it is faster, as well as causes the AI to respond faster in using it when commanded.
Pokemon would also have separate training and 'techniques' for contests, involving different 'show offs' and 'taunts' and 'dances' and stuff like that, and you can groom them and give them accessories and take good care of them to increase their health and appearance values.
At the start of the game you'd pick your character's hometown, gender, name, and some personality traits that would affect dialogue options and pokemon interaction and training to a small degree, and AI reactions of some of your pokemon, and some customizations like hair and eye color, hairstyle (which can be changed), and some initial outfits, and some personal stats, probably mental, athletic, and charisma, which can be leveled up to a degree, but you have different affinities and maxes based on the stater values, and you probably need high mental in order to develop psychic abilities, high athletic lets you hike around more and 'learn' stuff like swimming, cutting down trees in your path, and stuff like that without pokemon aid, high mental would allow this other ways thorough psychic powers, but limited by your psychic energy rather than physical endurance, and high charisma helps you interact with people and pokemon.
The game stats would be engineered so that while they have ranges that grow with level up, the amounts are relatively little, to the point that a lower level pokemon, perhaps if controlled by the player with psychic powers, might be able to beat a higher level wild pokemon by using skill and strategy and good gaming reflexes, or simply get lucky with AI behaviors, although they'd have less damaging attacks, slower attacks, and less HP and take more damage from enemy attacks, they'd still have a chance if they can get the right timing and control, like full guarding or completely dodging all enemy attacks and managing to hit the opponent enough while doing so. The difference between low level pokemon and max level pokemon would also be smaller, perhaps a range of 30% to 50% might be the possible range of levels for a Victreebell's slashing damage defense, but this would would vary from pokemon to pokemon, for instance a Blastoise might have a range of 70% to 95% for piercing damage defense, or a Charizard might have a range of 12% to 25% percent for water damage defense.
All pokemon would exist in the world and be obtainable without any special events or whatnot, although legendaries would be absurdly rare and nigh impossible to breed, and the entire pokemon world would be there, and you could travel around the globe. Each region would have it's own leagues, with badges and elite's, although they wouldn't necessarily be the same number of badges available, and different leagues would require different things from the badges, like Kanto might require 8 to go to the elite four, while the orange islands might require 4, and Johto might also accept badges from Kanto, but have an additional 8 gyms. Also, when you become champion of a region, you stay that until someone challenges and defeats you properly for the title, rather than having to face the same rival over and over again when you battle the elite four, and the champion can pick their own elite four from trainers they've met and defeated who have 8 official badges, and the gym leaders are selected by local competitions and a committee of local pokemon professors, and representatives from the local law enforcement and pokemon centers (nurse joy and officer jenny XD), so you can potentially become a gym leader as well, although to retain gym leader status you have to stick around the town and accept challenges at the gym regularly.
Trading or battling with other linked players adds their characters as NPC's to your world from the last time you dealt with them as an AI, which has different behavior and interaction with the world based on their transferred records and personality features and stats and such that they have, and some of their clothing style options, for instance if they have rich person clothes they might hang out with rich people or live in a mansion, and if they have winter clothes they might hang out in cold areas, like a snowy mountain, or beach clothes might hang out at a beach or on an island.
You can also earn money other ways that trainer battles, by accepting missions from people, getting jobs, doing trading routes, or getting paid a salary as a gym leader or elite four or champion for answering challenges and such.
The world would be populated by a bunch of pre-set AI characters, and some randomized lesser ones, for instance there would be random Team Rocket members, scientists, and Bug Catcher kids, but unique Brock, Misty, Professor Oak, Giovanni, Lance, etc. The pre-set ones would be favored by the game to maintain their positions in most cases, and have some pre-set behaviors scripted in more complex than available to randomized AI's.
Pokedexes would be purchasable, and you'd get a basic one automatically at game start which records the pokemon you encounter or capture, but have very minimal features initially, however, they can be upgraded in various ways, with purchased addons, awards for completing them certain amounts, catching or encountering specific pokemon, talking to certain people (like Bill or different professors), defeating certain trainers, getting more badges, winning contests, or completing special missions. The basic pokedex would have limited upgradeability, only limited memory, and a single 'old attachment slot' for addons, but you can get better ones which can take more and nicer addons, and have more memory for apps, either by purchasing them, or getting them as rewards for various things, being able to add features like cell phone service, items that detect what kinds of wild pokemon are in an area (perhaps by recording and analyzing their cries heard), or hidden items in the area, a calculator, a journal, a world map, etc. a scanner that analyzes pokemon footprints, and other useful or fun features, like simple games like Pokepong or Charizard Checkers.
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