For it to be a roundtable that lasts 90 minutes, it's gotta be something significant. We can comfortably rule out all games we already know about (like Monster Hunter 4), of course. We can also rule out franchises that are considered "minor" ones, like Wave Race, and probably also the ones that are purely enjoyed by a subset of Nintendo fans (like Star Fox).
It's at E3, so it's going to be something that appeals to the mainstream. But it's also a dedicated roundtable, going into depth about the game, so it's probably not a game designed for casual play (like "Wii Music 3DS", or Tetris). And it's on the 3DS, so we can pretty much rule out a heap of franchises that are already properly represented - NSMB, Mario Kart, Zelda, Paper Mario, main-line Pokemon, Kirby, Yoshi, etc... all rather unlikely. Oh, and if it's a well-known franchise, it won't be one that is typically shown off in Japan first (rules out other Pokemon titles, for instance).
This leaves me with three possibilities. First is Metroid - big enough franchise name to get time at E3, varied enough to get 90 minutes, core enough to have the time dedicated to it, and not yet present on the 3DS. I would call this the most likely possibility.
The second possibility is Miyamoto's new IP. We don't know what it is, or which system it's coming to, but it'll be something that Nintendo expects to have wide appeal, and it'll be something that the mainstream media will want to cover just by virtue of it being Miyamoto's game. However, being a new franchise, it'll require extensive coverage to begin the hype process.
The third and final possibility, in my opinion, is a third party crossover of some sort - we've had a few revealed for Wii U so far, but it's likely that there is at least one set for release on 3DS. If the franchises involved are big enough, it would definitely earn its position in a dedicated E3 roundtable. Mario & Sonic Adventure would be a great idea... but I doubt it'll be happening, given that we now know all of the Sonic titles coming from Nintendo's deal - I don't expect another Sonic title for Wii U or 3DS to be talked about until at least Sonic Boom has released. I'm not sure what else it could be in this category, but then, nobody predicted Pokemon Conquest, SMTxFE, Hyrule Warriors, or, back in the day, Mario & Sonic at the Olympics.