Masahiro Sakurai, co-founder of Project Sora, said that there is no way that they can't make Super Smash Bros. for both Nintendo 3DS and Wii U, in response to Iwata's reveal that Nintendo are making a new console.
This comes from the recently posted "Iwata Asks" article on Project Sora's website where he interviewed Sakurai about his future projects. Iwata approached Sakurai to ask which of the platforms they wanted to develop for, and was shocked when the response was both. We translated more of the interview and found out some of Sakurai's interesting ideas for the future Smash Bros. games.
Sakurai mentions that for him, just extending upon the previous Smash Bros games, putting in more characters, more levels, and improving the graphics because the hardware is higher spec, is not an option (in relation to the Wii U).
As for the portable version, he thinks it's attractive that they are inherently different from consoles so there are new possibilities that can be explored, although obviously these same aspects can lead to limitations for people who enjoy the Smash Bros gameplay as is. He sees portable gaming as more personal, gaming that you can make your own.
That being the case, for the portable version he wants to make it so that when a player plays alone they can get results from that, such as gaining experience and to level up characters, making them customizable. He thought that then you could take that character over to your Wii U and do battle with your friends.
For the portable game he plans on making it so that there is merit in players of varying ability playing together, as well as players who are good helping those who aren't.
In talking about the kinds of artists they need to hire, he mentions that he is aware that making the graphics in the same style as the previous versions would result in the characters becoming too tiny to see on the portable screen. (This seems to indicate that they would consider handling that problem through the graphics style in some fashion.)
At the very end, he mentions that if he can't find enough good people to make the games he'll have to cut it down to only making one (this Iwata Asks was posted on Project Sora's employment page, after all). Iwata mentions that this surprises him, since he announced it at E3, and then Sakurai backtracks and says , "Well, then instead it will take us like five years to make the game(s)".
So we can rest assured that the games will be ready before five years is up. Well, probably.