Dr. Mario, Dark Pit (and Lucina) aren't taking up character slots though. It's been said time and time again by Sakurai that they were last minute inclusions, and were originally skins for their "clone" character, but decided to make them their own character at the last minute. If they weren't included in the game, that's that. They didn't take priority to any character, or prevent a character from getting in the game. Without them, the game would essentially have three less characters, and not three different characters.
I only would see them as a "waste" if they were DLC characters, because that'd literally be a waste of DLC *cough*Lucas*cough* bye