Not the lower res/graphical fanciness, but the controller. It isn't that much fun to use as a controller because, well, it is fucking huge. It is a tablet. Thing is, if people wanted to play games on a tablet they'd probably do so and on one that could travel around with them.
Also it is pretty expensive. The screen, wireless interface, processor, all that jazz costs quite a bit and pushed up the cost of the Wii U. Part of what made the Wii successful was that it was really cheap compared to the "big 2" consoles. So people got it for kids or got it as an "and a" console along with their favoured of the bigger ones. This time though, the price advantage is not as much. It is still cheaper but not by as much.
So since the gimmick isn't something people are that interested in, and it drives up the price, it really hasn't been a good move. Despite being out a good bit longer than the Xboner and the PS4 it hasn't sold more.
Actually similar issue on the Xboner's side with the Kinect. That is the primary reason is costs more than the PS4, and that cost has been putting a damper on its sales. People just have no fucks to give about the controller gimmick, they wanna play games.