IC's were entirely made because he was looking for a retro character with a unique gimmick, which is solely for their double character potential. They were cut for one reason; they could not work with the 3DS' limitations. You're projecting your own bias instead of accepting the reality of what actually happened and was hard explained to us. Please stop making up stuff to justify them not coming back, especially when it makes no sense. The only thing that was noted was inefficient was the transformation characters, but that's not actually why they were split, which was also 3DS limitations. He basically noted that keeping them separated was also a good idea for balance, so an afterthought that is taken into consideration(and why there's a good reason to believe transformation characters like Zelda/Sheik won't be combined again).
Now, them not working well in 8-player Smash is a legit possibility(but was irrelevant anyway since if they couldn't get in the 3DS version, they would never be in the Wii U version. It was both or nothing).
Puppeteer characters, fyi, fully control the other character. Rosalina controls Luma entirely. Popo does not always control Nana, who has her own advanced A.I. and consistently makes decisions for herself. They also play extremely differently design-wise. Rosalina also is a very capable character by herself, having many strong moves, while Popo is heavily nerfed without Nana, removing not only the ability to properly Recover via Up B(Belay), but also removes their combo moves(and it's not just chain-grabbing either. Don't forget de-syncing is a thing, which allows Nana to do her own thing, making them a very unique fighter in their capabilities).
Two characters =/= Puppeteer. For that matter, IC's were made with the idea that losing Nana actually matters. It barely matters with Rosalina in the same way. They were made with beyond different roles and gameplay in-mind.