Dr. Mario doesn't have much going for him moveset-wise. I think if Sakurai feels the need to include another version of the main protagonist of a franchise, he'll make that character at least a partial clone, albeit, one who has a few differing moves, different weight and speed, that makes the playstyle between the two versiosn differ. Sakurai thinks it's important to have a younger version of Link, and Toon Link returned and does not appear to have changed much. Luigi is clearly far more important to the Mario franchise than Dr. Mario, and also already fills a similar role of being a partial Mario clone, (though of course the differences between Mario and Luigi are much greater than that of Link and Toon Link) so I really cannot see Dr. Mario coming back in any way aside from being an alternate costume for Mario.
The circumstances for Paper Mario would most likely be different though, as that version of Mario has extremely high potential, and I'd doubt Sakurai still cares about having a second Mario clone, so if anything, Paper Mario would probably be added for his high potential.
EDIT: Hmm, I forgot about Dr. Mario's Brawl data. Well, he WAS low priority though IIRC, so that does show Sakurai didn't seem to care as much about a second Mario clone in Brawl than he did Melee, at least not as much as a younger Link.