Many have claimed that this is because Judge Koh is heavily biased against Samsung, or for Apple. But really, it was Samsung's fault for fucking with the discovery process. At the federal level, the discovery process is the most important part of the case. It is sacrosanct. By ignoring their obligations in discovery, Samsung effectively killed their case because the Judge then disallowed the use of any evidence that Samsung did not make available during discovery, including, for example, pretty much all of the evidence that Apple copied others.
Lesson learned: if you have a bullet-proof case, make damn sure to honor your discovery obligations in federal courts or your bullet-proof case becomes an untempered-glass case.