I'm pretty sure PT's Pokemon were chosen too carefully to be switched around. I think it basically revolved around the Squirtle and Charmander lines. Blastoise is kind of similar to Bowser, whereas we didn't have a draconic character like Charizard yet. None of the middle evolutions are all that popular (I think Charmeleon is again on top there), so then it's between Squirtle and Bulbasaur. Ivysaur is quite similar to Bulbasaur, moreso than the other middle evolutions to their other evolutions, and Squirtle is pretty popular itself. So that's probably why things just sort of fell the way they did. Why we didn't have both Squirtle and Bulbasaur is probably just because Sakurai felt it was important to represent how Pokemon have different evolutionary stages, or at least felt it was a novelty he had the right opportunity to pursue.