Basically, when you are asked to select a pokemon in any scenario, make it so that you can press 1 for the first party member, or 2 for the second, etc, instead of having to click it. If this would require editing every single tree and dig spot and etc then I'm fine without it, but it would be so nice to have that number 6 hotkey for my HM slave instead of having to take my hands off the keyboard and move my mouse around. Also, making the options selectable in battle with arrow keys or WASD would also be a quality of life change, cause I dont want to have to take my hands off my keyboard every 5 seconds. Alas, if this would take years to implement, so be it, but I would really enjoy something like this. Make the mouse less dependent for the game. It is based off of Pokemon, after all, which has no mouse (At least up till the DS where they had a touch screen) Also, make the selection not show up until WASD/Arrow keys are used to select something.

Inside battle you already can do it. Pc version - the 12345 are for hotkeys. Inside battle 1234 have others functions, 1 fight 2 choose Pokémon 3 to bagpack 4 run away. Also inside every execept the bagpack you can choose by the same keys what u gonna do. But yes besides this I agree with 1/2 things u said up there.