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:
The size of the sensor is the most important thing.. the bigger the area that can capture light, the better. The pixel size vs. pixel density is an ongoing debate... Nokia went with pixel density, and I think its the right call for mobile devices. There was talk that they will go even further with 60-80Mpix count.
Most DSLR (Nikon D8xx being the exception) still bet on fewer, but bigger pixels.. generally that gives you better dynamic range and arguably better low light performance.
So, like most things the best choice is probably somewhere in the middle, but we will have to wait and see.
You can actually watch how Apple is going to start pushing bigger pixels instead of pixel count with the next iPhone.. going by the rumored Sony sensor, and according to my calculations, the iPhone 6 will come with ~1.9 micron pixels and Apple are going to go on a marketing frenzy.. it will be fun to watch.
That being said, I expect the new iPhone to perform extremely well.. I expect great dynamic range and decent low light performance. The only question mark is the optics .. that narrow/square look is unacceptable, let's hope they can match Nokia. The other thing is the flash.. no xenon = no flash
Back to the sensor .. just look at this for example
Notice how the GS5 had to use a much higher ISO in order to gather similar amount of light compared to the Nokia device.. light gathering ability is very important