On one hand, Advance Wars hasn't had a single entry in over 6 years -- and the last entry left the series in an unclear point as far as its identity is concerned. On the other hand, Fire Emblem is on a momentum, with Awakening having been a great success, and Smash Bros. having promoted the series' characters in a rather loud way.
If it was up to you, which series would you bring next on 3DS? I have very little doubt that there will be both an Advance Wars and another Fire Emblem game on 3DS -- especially now that it's lifecycle has been extended through the revision. But for the sake of conversation, let's say IntSys would only have time for one of them.
If I managed IntSys, I think I would go with Fire Emblem. The opportunity is too good to pass on; the series is quickly climbing up in the hierarchy of Nintendo franchises. It has the potential to become even more iconic and successful, but that window of opportunity isn't going to last forever. I think "Awakening 2" (or Chronicles / Reckning / Legends / Whatever), directly succeeding the first game seems like the way to go. Throw in Lucina as one of the main characters, and they will have the interest of many people.
Personally though, I'm more hungry for a new Advance Wars -- especially if it was like the classic ones. A game with a similar narrative to FEA but a more "cartoony" premise is something I could get into.