Yes, very true. My main stories (Rival's Story and Dragon Days), I've been pretty limited in what I can give my heroes but usually I prefer Pokemon that aren't obviously used in a certain way.
For instance, the star of Blue's team was probably his Alakazam, which you wouldn't necessarily leap to. Erika had a pimpin' Tangela. Rex's Poliwrath in Dragon Days is a bit of a bad ass. I agree wiht you completely, SCND.