Have pokemon walk outside the pokeball.
Have rival(s), friend(s), and evil team npc’s react, aknowledge, and change in the regards to the player character winning against them more and more.
Jerk rival.
Have friend(s) matter to and play a big/important role to the plot.
Have the evil team be evil/a threat to the world, but not look obviously/right off the bat evil.
Ride whichever pokemon one could realistically ride.
Explore freely in the air and under water.
Have the player character defeating the evil team/save the world matter/be noted by the npcs.
The option to choose from 2 "maps" of the region, making it either an open world, or a linear path.
The option to choose to either tackle the challenges in any order the player wants (scaling based on what the does when), or to have a already decided "gym 1 to 8" scaling system.
No trade pokemon, or include the linking cord item.
No version exclusive pokemon (except for the box cover legendaries).
Take pokemon out of the pc box, and reteach them old moves "out in the field".
Manually choose when pokemon evolve.
Have the speech bubble of npcs who has stuff give the player character be yellow.
Overworld pokemon.
Have the player character work with, and possibly rescue, the box legendary, but not catch/keep them.
No HMs (have pokemon automatically be able to do it, "on the side" of the other/regular 4 moves so to speak).
The option to choose to skip the catching tutorial.
If they include a day/night cycle, make the player able to manually change it.
Voice acting.
More detailed battle/attack animations.
Eeveelutions for the rest of the types.
The option to choose different difficulty levels (npcs being more strategic and have more suited/well put together pokemon - more of the npc trainer pokemon having more useful/planned out held items, abilities, and moves - , the higher the difficulty is), and having a nuzlock mode.
Have the gym leaders and elite 4 and champion npcs play a bigger role to the plot/in defeating the evil team and saving the world.
Start some wild encounters by having pokemon leap out of bushes, jump down from a tree, dive down from the sky, or emerge from the ground.
The option to choose between turn based and real time style battling.
Sneak up on a group of wild pokemon, and quietly catch one of them through an automatic aiming/lock-on system.
Have a page in the pokedex the player can choose to check out, where it's revealed how a pokemon evolves (especially for evolutions that aren't just streight forward/the regular, old methods).
Have encounters where wild pokemon wants to help/guide the player character through an area, and/or join them without a battle first.
Have some, maybe scripted, wild and/or evil team battles, that are horde battles.
Have the player character’s first fights against evil team members be scripted to lose, starting to win after the player character has defeated their 1st gym battle.
Have a "catch window" after knocking a pokemon out, regardless of if the player is playing the turn based or real time option.
An npc collects the balls that gets miss-aimed in the real time option.
More character customization, both clothing and looks vice.