Most people I've seen prefer the 3ds version, and if you plan on getting Monster Hunter 4 when it comes out it'd be best to get familiar to the 3ds controls, go for the 3ds version I say.
Wii u has sharper controls due to the 2nd analog stick. it's also is nice hd if that floats your boat, they are exactly the same game with the exception being WII U has online mode.
I prefer soloing the tavern missions so 3DS is my pick.
but controls are slightly better on wii u, and the 3DS has the added benefit of being portable.
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