Assuming you had the original Red and Green source code, the programming and Japanese skills to change it to your whims, and the means to replace files with your completed code any time during Red and Green's development, what would you do? Keep in mind your changes would still be subject to past technology most noteably Gameboy cartridge sizes. I'll start.
> 1%ish of a Random Mew encounter in any grass as first encounter after beating champion with 150 Pokedex
> Flying type Specialist Team Rocket admin
> Bug type Specialist Sparring partner at Indigo Plateau
> Post Game Proffessor Oak fight that uses a Normal team plus the third starter
> Buffs to all Pidgeot's stats but attack
> Fix ghost type and give Ghastly line a 60 power ghost moves that lowers all stats of a Psychic Pokémon hit by it.
> replace DVs with random values that reduce or increase stat experience for different stats. Use extra data for more item storage.
> Bronze, Silver and Gold membership shops at Indigo Plateau that sell all TMs, pp restoration items Gym leader rematch tickets, elite four level increase tickets, and level 5 base trade/gift only Pokémon you have fully evolved level 100 versions of that require a shit ton of money to use and unlock
> change all the learnsets of the Pokémon used by the Elite Four and Champion to gurantee they all have decent movesets (the player would have to grind a shit ton to get these movesets for himself anyways).
Maybe I got too ambitious and broke my own rules lol