Last night (actually Noon in Japan), Nintendo held a conference highlighting the 3DS. During the event, it was confirmed that Intelligent Systems is developing a new Fire Emblem for the 3DS. While there is still just a working title for the game, it was announced that the game will release in Spring 2012. No story details have been given at this point, but the names of the three main characters were shown: Ronku, Liz, and Amelina. Along with updated graphics, there appear to be new gameplay features, as the videos show two characters attacking at the same time.
Nintendo's Japanese 3DS Conference site has screenshots and a couple additional gameplay videos available to view here.