A few rambling thoughts.

I recall many years ago when UA would occasionally run a 747 or two at night LAX/SFO on horrible weather days to help catch up with the sea of passengers that were delayed for hours, and these aircraft would otherwise be on their downtime.
I recall various times many years ago when I'd either cancel a trip while at SFO due to a certain misconnect on a short-duration trip, or otherwise suffer long delays (to/from), especially on shorthaul flights.

So, this is nothing new, and I've lived in the area for over 30 years. But I do think other factors are compounding the delays, and it isn't the specific fault of SFO.

Have you flown in/out/through SEA or LAX recently? They are so severely impacted by overcrowding, insufficient gates, overcrowded taxiways, and so on, that there's a cascading (no Pacific NW pun intended) effect on all these airports, including SFO. This may be magnifying the historical SFO delays to which we're all accustomed.

Doomed? If this were the case, EWR would have shut down years ago.