States can indeed decide to reform their primary systems. Just this year, for example, Minnesota changed from a caucus to primary system in response to widespread complaints about the practice. Reform is difficult, of course, but if there is widespread desire for it at all levels, it can be done.
There's a very simple way to change the system so that every vote counts: count every vote. The idea that some votes literally do not count should be unacceptable to Americans or anyone who believes in democracy. The system needs to be changed to ensure that every vote matters, or the United States is not a democracy.
Many have learned about the various archaic rules that several states impose over primary elections. Whether its complicated voter registration requirements, or how votes are counted, the primary system seems to be broken in a lot of states. The collective will of the voters could change the primary process to make elections more fair; ensuring that every vote counts.
It's outrageous that after so much time that millions of ballots remain uncounted. When machinery can't do the job, human hands still can. In a state as hard pressed for jobs as California usually is, it should be easy to find enough workers who can pass a background check and certify with the state board of elections to sit in a locked room and count or sit and watch computer screens while the computers count.