Clinton>Mukilteo is pretty tough, especially from April to October. Most of the time in the summer it's much faster to just drive allll the way up Whidbey and then allll the way down on the 5. I'm sure there's very valid reasons for why they never built a bridge (it being basically unused for half of the year being one).

Edmonds>Kingston is also a crapshoot in my experience. Half the time it's fine, the other half they've cancelled the run.

I absolutely love the ferries, but I always have my Plan B.