The difference here is that Dr.Mario isn't as big a deal as either Link. Both are by leaps and bounds more iconic than the doctor persona of Mario. In context of what is more important to the respective series, the Link's make sense. Dr.Mario does not have the same reasoning behind him, nor does he have the star power that any version of Link does.
Link is Link is Link.
Doesn't make any difference what age he is, it's JUST LINK.
To find excuses as to why two of him are acceptable and not two of anyone else is hypocritical.
It's not like either Toon Link or Dr. Mario were anything more than easy clone fodder anyway...(though if cednym is to be believed, Dr. Mario was picked for being from a critically-acclaimed retro game, his games' music, and
because he was a doctor.)
The reason why I find Doc highly unlikely at this point is because I personally believe that 6 Mario slots is a bit much.
Being unlikely is not what I'm referring to (since I feel that Rosalina put a huge roadblock for other Mario characters). It's that you argue that he is unwarranted while Toon Link is.
And then again, considering how Sakurai treated Dr. Mario elements in Brawl, it could just as easily be that Dr. Mario would be a "Dr. Mario" character rather than a "Mario" one.
Toon Link is an exception. That's basically all I think there is to say.
Toon Link is just as warranted as Toon Zelda/Toon Sheik.
As in, he isn't. But, he's in anyway. Dr. Mario, being featured in Smash before, wouldn't be any worse.