How would you imagine the third gen games if they stayed faithful to the first 2 generations, and not some kind of reboot?
These are the first things that pop into my mind:

- Legendaries going back to being side quests and a reward of exploration, and not the core element of the plot. Legends, indeed, and not increasingly strong monsters acting in the public eye.

- Antagonists that don't have to be clones of Team Rocket calling themselves "team+something." Either continue with the Team Rocket story, or think of something new.

- Just pokémon that maintain the minimal, caricatured style of previous generations, without too much detail.

- Real animals existing in the storyline and dialogues of the game, just as you can find grass pokemon along with real trees and vegetation.

- Real-world references. The pokémon world continues to remain the real world, with the variation of the mysterious arrival of pokémon in ancient times, which altered some events. Not a world magically created by a pokémon as it has become over the years.

- Appearances of characters from past generations, with plot references from previous games.