Justin, I'm not sure what you are suggesting would work - sort robbing Peter to pay Paul: you're saying either run late with a full load, or leave early with few vehicles, but both mean few vehicles per hour getting across. 

Part of the issue is the Olympic class ferries can make the runs on time - I was on the boat one time that made it across in 12 minutes! (there just happened to be a state representative on board!) - but they are highly fuel inefficient when run faster, and WSF is not allowing them to operate this way so they don't have to pay more for fuel. 

What erks me, however, is that your paper jumped on the 2-big-boat solution without looking at the facts, and you went so far as to make stuff up instead of providing facts: for example, you said that there is a pedestrian safety issue at the Clinton dock (not true) and that the problem is because the boats are different sizes - as if there is a giant see-saw across the water that has to be equalized (again, not true).