We have gotten confirmation from Capcom that the Wii U version of the game will be available in 1080p, a major boost in resolution over the 3DS version. This is to make sure that the game still looks crisp, even on your big TVs. The game will also have it's sound enhanced as well, now having linear PCM 5.1 surround sound. So feel free to get you fancy speaker system hooked up when you play. In addition to this, the Wii U version will feature online multiplayer, while the 3DS version is limited to local multiplayer. There is still a good reason to get the 3DS version though! You will be able to transfer save data between the Wii U and 3DS games, for when you want to hunt monsters on the go. You can also have up to three 3DS play local multiplayer with the Wii U, to make a four man hunting party.
Credit to XuNiNukaza for the source.