The amount of ignorance in the last pages is just astounding.
Anyway, it's what was suspected all along. Just like Lucina, Dark Pit and Dr. Mario were originally intended as alts rather than separate characters, but minute changes made them their own slots, due to technicalities.
Sakurai said:
Since their functionality had differences, forms were separated from each other. However, it was vital that this didn’t increase the required man-hours. Some relative tuning was sufficient as it wasn’t necessary to create balancing from scratch.
While separating the characters, they wanted to be sure that not much time was dedicated to them, hence why they're so similar. As for Dr. Mario, it seems they went the extra mile to recreate him from Melee by adding the Tornado and Megavitamins, as to not alienate Dr. Mario fans.
Sakurai said:
Could you please leave it to me to select [characters] with man-hours and costs in mind?
With man-hours and costs in mind. This is a very important factor in development.
They have limited budget and time. Things have to be prioritized and scheduled carefully. This is why cuts happen and ideas are scrapped, not because "SAKURAI IS A DICTATOR THAT HATES THE FANS!!! D=<" as some people here were implying not so subtly.