The theory that HTC is applying to their smartphone cameras is ok, not only resolution (megapixels) is important, sensor size is vital too. Since on a smartphone you have limited space, sensors can't be that big, and so HTC has developed that technology.
It's something similar to what Nokia did with the 808, they put together 7 pixels to form one, that way they could reach that crazy resolution + quality.
The main issue with HTC is low light conditions, ultrapixels are bigger and are supposed to catch more light, but that's not the case and lack of OIS make performance even worse.
Honestly Nokia has just way more experience developing smartphone cameras, even the 520 has a great one.
Carl Zeiss lens are just wonderful.
Oh, and your can really notice why HTC used two rear cameras on this pic: