We've sailed out of San Francisco several times and each time the terminal boarding and disembarking was just awful! Confusion was king!!! I mean it's bad in most cruise ports we've been to, but somehow San Fran seemed the worst. Not enough room for passengers on the sidewalks, NO parking to speak of...no directions or help from any staff off the cruise ship or San Francisco...just 'everyone off the ship' and it's up to you to find your way out of the masses of people.
But I don't know if staggered boarding is the answer...especially if WE'RE relegated to the late boarding. (hahaha) There isn't really anyplace to sit and wait to board...the pre-boarding area is unusually small and always crowded.
(can't remember what Seattle was like...but I sure remember S.F.)
We like getting to the ship early, boarding, walking around, having lunch...it's part of the cruise ritual...part of the fun.
Plus, I think there may be exceptions made for certain cabin levels, and for the 'on lookers' who are not included...well, you will have some angry passengers.