User blog comment:Dan12322/Mario Franchise in Smash 4/@comment-4115159-20141230174135

Also Dr. Luigi should not be Doctor Mario's alt. The point of palette swaps is that despite resemblance to other characters, the fighter remains the exact same in their attacks and stats. if the stats were to change then they'd make that palette swap a character of their own. That's why Marth and Lucina are seperate. If Dr. Luigi was a swap of Dr. Mario then he'd have to have his stats and it'd be kinda awkward to play as him given that he would have Mario's stature and animations. If anything he would be a swap of Luigi because they are exactly the same except the coat.

Also, the examples you gave do not apply.
 * Zelda and Sheik are literally 2 separate fighters; even in Brawl. They just share a character slot and can switch mid-match.
 * Bowser Jr was given the clown car for a reason. So that the stats can stay the same no matter who uses it. If he were fighting on foot the koopalings would not be swaps.
 * Olimar and Alph are very similar in size and shape, so much so that they could just give them the same stats in Smash.