Hey, good point. The only thing that could possibly explain it is Luigi's personality. Between Melee and Brawl, Luigi finally became something that wasn't just 2nd Mario. He became more cowardly and the quirkiness in his voice reflects that. Just as a question, had their been any other game where Luigi sounded just like a higher pitched Mario? It might just be because Luigi had NEVER sounded like that. Again, at least Bowser and Donkey Kong had this excuse at first.
For the point on Dr.Mario, he was just one of the 6 clones chosen. Easy to make and include. They needed at least a few things to change him up, and this was one of the few ways. But hey that's just speculation