This areticle says, "The late departures have led to longer waiting lines, according to the press release." It would seem likely by this wsdot release (below) that dramatic increases in ferry vehicular traffic have led to longer waiting lines. 
http://www.wsdot.wa.gov/news/2017/01/18/ferry-ridership-surges-highest-level-decade
I would think that most Mukilteo/Clinton travelers are less worried about the ferry's on-time record as they are about the amount of time it takes them to get onto a ferry. 
Exploring new schedules should include jettisoning the schedule during peak hours on peak travel days through the summer season. Load and unload the boats quickly as safety permits, and then move them as quickly as reasonable across the water between Clinton and the mainland. If this speeded-up transit results in greater fuel use, I think most car owners would gladly pay a fuel surcharge of an extra buck or two to avoid sitting in their cars for an extra hour or two.