Okay, so
>Not split into two versions. Make it one version without version exclusives if it's meant to be more console than handheld and make it the definitive Kanto experience
>Don't make it grid-based
>Actually have battles
>Have a free camera
>Increase the size of locations in a way that makes them feel more natural and gives them more content while still staying true enough to the original layouts (Viridian Forest being a winding path as an example)
>Overworld Pokémon would be fine in this scenario since you don't have an overhead view, and the player should have stealth mechanics like sneaking
>You can have battle transitions, but make them more natural like showing the world changing around you and the target Pokémon
>Put far more focus into the animations behind the Pokémon present in the game
>Include all cross Gen evolutions, forms, and and Mega Evolutions for Gen I Pokémon
>Include the 40 cut Pokémon from Capsule Monsters with various areas rebalanced to include them
>Choose Bulbasaur, Charmander, Squirtle, Pikachu, or Eevee as a starter, but make it possible to obtain them all without trading
>Allow online trading and battling
>Make battling the standard
>Don't make it so damn easy
>Just go back to Red, Green, and Blue and have the other protagonist at least appear in the game
>Have Sugimori handle the artwork and try to mimic his old style
>Let Masuda handle the music instead of Kageyama
>Add new side areas like a volcano or a Battle Tower
>Let the game remain as open as they originally were without making it more linear or story focused
>Add in more optional story material and side quests
>Difficulty settings
>Trainer rematches
>Stadium mode where the starters can learn their signature moves as awards, Pikachu can learn Surf/Fly, etc.
And so much more.
You can make a Kanto game with a focus on Gen I Pokémon in this day and age and still make it great and the definitive Kanto experience, but there was nothing great or definitive about LGPE.