That's not it. USB specification limits the power output a USB port may have. Some manufacturers and devices go around this (e.g. Apple), but in the end it's all about conforming to specifications as required by the license to use technology like this. Manufacturers only came out with Y-cables to workaround this limitation. It never was an actual solution to the problem, but it stuck and people started using it. Remember, Nintendo even recommends to use an externally powered HDD with its own power adapter.
I get that but that doesnt stop Nintendo from allowing their ports to push out more power. The ports on the original Wii push out more power than the ports on Wii U. I have yet to experience the force shutdown from too much power draw on Wii that I have (twice) on Wii U. The USB power limit on Wii U is just a pain in the ass and the lack of ports is just as frustrating.