I'm not a fan of Dr. Mario for a lot of reasons, since he represents all of the worst aspects of a clone IMO. He's literally the same character as another, his move differences are arbitrary and have no necessary background context in his original games (unlike Luigi, who was a clone of Mario in 64, but his "similar yet different" nature had context in the actual Mario games). And in Melee, he just seemed better than Mario across the board, making Mario feel less relevant.
"Him being an alt would mess up the records" is clearly not a problem, since Alph and the Koopalings are alts, and Sakurai had no problem doing it with them.
I know clones are just extras and all that jazz, but the particular implementation and choices for clones this time around, are absolutely terrible. Speaking of Alph, why does he get to be a mere alt, yet Dr. Mario, Dark Pit, and Lucina get to be arbitrary clones? Alph could have easily been one of the most interesting clones (not even semi-clone, outright clone) in Smash history, with minimal effort, and has that given context in Pikmin 3 for being "similar yet different" to Olimar. Keep his normal attacks more or less the same, but make him have Rock Pikmin (BTW I hate how Sakurai actually teased us about this, saying "he doesn't have the Rock Pikmin" when that much was obvious when he was being announced as an alt. Makes it obvious that he WAS considered) instead of Purple Pikmin, and also maybe give him the Winged Pikmin instead of the Albino Pikmin. Rock Pikmin could have poor horizontal range, but are thrown at a slightly more vertical arc, and could be a Meteor Smash if they hit opponents from the top, being kinda similar to Villager's Bowling Ball when thrown Winged Pikmin could have infinite horizontal range and multi-hits when it connects, but will basically fly off screen if it doesn't hit a wall. And instead of the Winged Pikmin recovery, give him an improved version of Brawl Olimar's recovery (they could probably work the Winged Pikmin into it to improve it - though this change isn't even necessary). And then just give him different organisational properties for the Pikmin and what not.
There are are a bunch of better clone characters I could think of, but Alph serves as the best example simply because, for some strange reason, he was relegated to an alt.