Without diving into the specifics, I don't see a problem here. The iPhone was hugely innovative, and there was a lot there that was genuinely new. While in general I'm not a big fan of patents (often the 'innovations' covered are trivial), in this case I think that Apple sort of deserves to profit from their R&D. Clearly, some of the HTC phones are knockoffs.
Well, i see a BIG problem... Apple's cell phone patent portfolio is very small, the only thing they have is some UI/multitouch patents.
On the other hand, companies like Nokia-Siemens, Alcatel-Lucent, Ericcson and Huawei have a huge amount of cellphone patents, if Apple doesn't cross-license its tech, they will be screwed for sure... Also, i bet HTC has more patents than Apple...