You don't need to include every single Pokémon from whichever generations you choose to use. For example, I wouldn't include Diglett/Dugtrio or Dragonite in my game because I'm not too keen on them aesthetically, but I would include other Gen 1 Pokémon. Other people may love Diglett, but I don't care because it's my game.
As has been mentioned, just choose which Pokémon you like, and if possible, make sure there's some kind of balance.
It's a very good idea to not throw all existing Pokémon into a single region anyway, because there are far too many and it would overwhelm the player. About 150 per region works just fine.