Here is my list of things that would improve the mainline series:

-pokemon visible in the wild
-battle starts with no transition
-battles are only double battles
-no double versions
-every playthrough has a unique seed that determines encounter rates
-every game has a save file for a playthrough, and a second save file where caught Pokemon are stored to be imported to playthroughs
-battles are reworked to be very stylish with hundreds of varied animations multiple per attack
-super effective moves no longer one hit kill an opponent
-instead it knocks them down and staggers them allowing follow up moves
-moves are displayed at all times in a radial menu so one button press is all that's required
-moves are equipable outside of battles
-five moves can be equipped to a Pokemon
-always have access to every learned move, it just requires more button presses than the equipped
-no more IV stats every Pokemon is 'perfect'
-no more shiny Pokemon
-each Pokemon has several variants including regional ones
-starting Pokemon choices are much more variable and based on seed
-choosing the starting town, and non-linear progression