A lot of this is the fact that the Wii U is new, and will take developers a little more effort to learn.
But also it does have its foibles, although it has more memory than either the 360 or PS3, memory access is quite slow except to the eDRAM, which is only 32MB, so some things are harder to do with it than they are with other consoles where main RAM can be used for them (noticably, Batman: Arkham City has lower quality shadows, and some games lack antialiasing).
In time, Wii U versions of things may well be better than both of the previous generation HD consoles, but not yet. (Mass Effect 3, for instance, runs at a consistently lower framerate than the Xbox 360 version).