An internal Nintendo software team is making software for their own hardware? Wow!

Has to be a Paper Mario, which can either be a really awesome thing or a horribly bad thing.

Super Mario RPG 2 or bust.

Here's what we know:

Fire Emblem Awakening released in April 2012 - Intelligent Systems
Paper Mario: Sticker star released in November 2012 - Intelligent Systems
Game & Wario - Handled by Nintendo SPD and co-produced by Intelligent Systems.
SMT X FE crossover - Handled by Nintendo SPD - development by Atlus and co-produced by Intelligent Systems

There are most likely two unannounced projects being developed by Intelligent Systems currently, excluding SMT X FE, one being a Wii U, the other a 3DS game.

I'm leaning more towards a 3DS Advance Wars and a New IP for Wii U. The producers of Fire Emblem have previously said that they had thought of bringing Fire Emblem to a more modern or sci-fi setting. FE X SMT will allow them to explore a modern setting, however they have not explored the sci-fi aspect. Maybe a new IP to explore such a posibility of a sci-fi world?

It's likely to be something new. Intelligent Systems is a golden developer to Nintendo because they can deliver many high quality games I'm a short time span. Sadly, all tier major four franchises have been stumbling lately. Advance Wars' sales dropped to the point that the series was either killed off or left for a prolonged period of no games. Wario-ware dropped to the point that it's been relegated to download-only, and even their oldest and most fundamental franchise - Fire Emblem - was going to be killed of unless FE13 was a success. (Additonally, PM has lost its acclaim as a top-of-the-line series, but it's the one holding up best overall). 

They're not making a console Fire Emblem. They'd be utter idiots to. The series popularity has been vaning ever since the first game released in the west (FE7). When you finally make a success, you don't ditch that to try what failed to be a success twice already. 

What they have done - to huge success - is downloadable games. Pushmo/Crashmo are their biggest successes in a long while, barring FE13. A new form of puzzle-strategy game utilizing the gamepad seems right down their alley. 

The most likely type of game - by far - is a quirky, fun and rather strange eshop title. 

A sci-fi setting would better fit Advance Wars, to be honest. :P

RealTimeStrategy game please. Make the gamepad the perfect controller for RTSs

Kick Halo Wars with its lousy 82% from the throne of console RTS games! gogogo! (I like halo but 82% for the genre king is quite sad)

Here's hoping for FE on the Wii U.