Without question, it has a few issues. This version of ME3 seems a lot less visually stable than, say, the Xbox 360 version -- the frame rate is choppier, the animation seems rougher. The audio suffers, too; while the music and sound effects have come over fine, all the dialogue has a hollow, echoing quality to it. The GamePad's analog sticks aren't as comfortable as the 360's, and the placement of the face buttons relative to the right stick made me continually miss the melee and reload buttons. My headshot ratio has dropped precipitously. It's tragic.
Now, the Wii U Controller Pro rectifies some of these control issues -- it's pretty much a 360 controller, and it works great. But the problem there is that you lose the GamePad features if you use the Pro, and the GamePad is actually used pretty well here. By default, it serves as a quick skill-select menu or live map display (yes, just like a DS game), and the developers have added some neat details -- for instance, during the prologue sequence, the map display breaks up and distorts momentarily whenever a Reaver in the distance fires an energy blast. There was some actual thought put into this port, which is always nice to see.
The real advantage to the GamePad, however, is the fact that the game looks much better on its smaller screen. I don't know if it's the flaws being obscured by the pad's screen when they're shown more clearly on the higher-performance LCD of an HDTV, or if it's simply a benefit of the pad's lower resolution requiring the system to render fewer polygons, but the game plays noticeably smoother on the GamePad screen. The stiffness of the characters doesn't come across as readily, and the compactness of the visuals makes the environments seem far more beautiful and detailed.
Another trade-off: The Wii U version comes with all the collector's edition exclusive content on-disc already (though not high-end DLC like Leviathan), but much of the subtlety of the game is lost due to the lack of support for Mass Effect 1 and 2 save files. The game kicks off with a 20-minute digital comic that allows you to make key choices to shape the plot, just like the PlayStation 3 version of Mass Effect 2, but the most interesting moments in ME3 came as outcomes of smaller choices that aren't included in this prologue. So while you'll still shape the outcome of, say, Tali's major plot arc, you'll never know the pleasure of helping Conrad Verner find true happiness.