(I'm on mobile, so I can't reply to multiple people.)
Re: FLUDD not making sense for Dr. Mario: really, none of Mario's moves do. In his games, Dr. Mario doesn't really do anything; he just stands off to the side while the pills drop. So in terms of what makes sense for the character, I'd say the Tornado and the "Medicine Shooter" make equal sense.
As for what's easier to do, I'm no programmer, but I'm pretty sure it's easier to take Mario, slap a coat on him, and tweak his properties than to go changing his moveset. So if Dr. Mario is the result of having just a little time left over, I'm sure they'll make him a straight clone.