Your friend, Saint7 Got a fair amount of mail back on Mr. Blackie's letter, and this was the least inflammatory. Since I already said my piece about this yesterday, not much more to say, just wanted to point out the opposition. I doubt Nomura had any say if the characters were super deformed or not. Amano's character designs in all the Final Fantasies, including the NES ones, were drawn to scale, yet were super-deformed in the game. It was most likely the higher-ups at Square who chose to have realistically proportioned characters.
Character designers are under almost direct control by the producers and directors of the project.
Pick your favorite. This stuff is a lot more calculated than many people think. Maybe Nomura's characters look alike because they had the best response out of a japanese test group. Maybe that explains why Tidus's hair is blonde now. Gameplay also has to come into consideration.