I know that I'm not the creator of Fire Emblem, but given that we haven't seen one for the Wii U yet, I have a (hopefully) unique idea as to how they could implement it.
Make the bottom screen a lot like the GBA games in terms of layout, with the top down map perspective, and you'd use it to control the units. Given the bigness of the gamepad screen, they could have some basic stat menus and such on the side, and with one of the buttons you could expand them to pull them out entirely and see them in detail.
On the big screen, you'd have a lot of camera angles going around the map, somewhat similar to how it works in FE: Awakening. The map and units would be in detailed HD graphics, and it'd really look cool once they get into battle. The way I see it, it could all be continuous without needing to switch between the big map and the small battle scene, which would be pretty innovative for the franchise.
What do you guys think?