They added specific lanes for nationals to use; nationals are the taxpayers therefore they're the ones who are most listened to. As a consequence the nationals lines were always fast and well staffed, while the international entry lines grew longer and longer.
If they hadn't have split the lines, everyone would be on the same "side" and complaints from nationals would result in improved passport control for everyone.
There were big (permanent) signs up directing us to a citizens line and a noncitizens line. They weren't taking that especially seriously; there was also a staffer at the fork directing citizens into the noncitizens line and noncitizens into the citizens line.
My guess is that this was an attempt to balance the waiting time in each line. It was a horrible system, largely because the system was barely able to admit noncitizens at all. Both lines crawled as the noncitizens stepped up to a booth and were s-l-o-w-l-y fingerprinted and eventually waved on their way.
Contrast what happened just a couple weeks earlier when I entered China. Fingerprinting was required for entering noncitizens there too. But you didn't have it done at the booth while everyone waited in line behind you. You got yourself fingerprinted at one of a row of unmanned machines, got a receipt from the machine, and then went to get in line. All the immigration booth did was take your receipt.
I had the misfortune of arriving on an international flight to SFO when they first got those booths. Some official decided to constantly shout and berate everyone trying to figure them out (he would keep contradicting the screens, or interrupt people trying to read them etc). Thankfully I haven't experienced that since.
And it used to be a lot worse. Instead of a single long queue, there would be long separate queues for each desk. It became quite an art trying to deduce which lines would process quickly.
But when you use the Chinese fingerprinting machine, you're not holding up the immigration line. This makes a big difference in queue times! SFO is wasting an incredible amount of passenger time by making everyone in line wait for everyone else to get fingerprinted.
They also seem to have a wide range in staffing levels, and adjust what is "open" based on that.
You are right about the efficiency. Quite simply none of the people involved at that level have any incentive to improve it. It won't improve their pay and promotions, and the less efficient the bigger an empire can be built by managers.