You mean like Squirtle would not play well on the Metroid lava stage and stuff like that? I don't think it's a problem since you could whip out Charizard, who wouldn't get burned as badly. PT and Olimar have other options.
Looking over the characters, I don't really see any other characters being affected by elemental abilities (except Pikachu if they really want to extend it to all Pokemon) so what I'm saying is that the characters with more than one option should have strengths and weaknesses. If they were all the same in terms of ability, why bother switching one for the other?