Have Venusaur and Blastoise be region 2 and 3, but you get called back to the Oak Ranch to deal with them since they're also Red's. Then after region 4, you get called back again for a scene with all three.
I remember the pokemon canon time [in the show not the game] that ash, misty, brock meet a island full of squirtle, wartortle and that one alpha pack blastoise I think you can make that
