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?
Just stop to think for a minute about the two platforms in question: One is a handheld that's (IIRC) not even as powerful as the Wii, and developing on it severely limits what you can do as an artist. The other is a console vastly more powerful than the Wii, where Retro would pretty much be freed of all restrictions for all practical purposes. Retro's a developer highly experienced in high-quality, extremely time-intensive AAA console development with major artistic design. Yeah, I'd really want to waste
that talent on a device as weak as the 3DS and a platform that doesn't play to Retro's strengths as a developer. Plus, after today's Press Conference it's painfully obvious that Nintendo needs more major 1st party Wii U releases, so why use your best studio on a 3DS game?
Besides, if there's one thing I've seen time and time again, it's that handheld developers tend to make the best handheld games. Console developers tend to make the best console games. Considering how long it takes Retro to make anything, I want them working on a project where their talents can best be put to use, and they aren't a large enough studio to split their resources working on more than one project at a time. Retro is wasted as a handheld developer, working on games that other Nintendo developers could easily do themselves.