Man, I hope not. Putting a team as talented as Retro on a 3DS game just seems like wasting their considerable abilities. And if that were the case, I don't see why Nintendo wouldn't feature that game in the press conference.
I just don't understand this line of thinking with the general core gamer. Since when has a handheld game become "less than"? Why does a game becomes superior just because it forces you to be tied down to a big screen TV?
It's like when people complained that RE: Revelations should have been a console game. Porting Revelations to the Wii would not make it more enjoyable in any tangible sense.
/rant
I would assume the reason they would not show a Retro 3DS game during the conference was because they planned to save all new 3DS material for the showcase. Scribblenauts aside because that was announced for the Wii-U as well.