The separated thing is super interesting to me. Obviously we couldn't do it on all streets, like the very skinny SF ones you talk about (I live near many of them in the Lower Haight). On those, which are not major thoroughfares, mixing bikes and cars is fine. But when it comes to a 4-6 lane street like Market St (or some in Chicago), separated makes sense. The traffic will go around if the street is less amenable to them. It's the same argument as taking down a freeway through a city. SF did it both at the Embarcardero (well, that one was by natural causes aka an earthquake), but then also at Octavia. Traffic slowed, neighborhoods revitalized. Studies have been done showing that taking these down doesn't greatly increase driving times, and often the traffic driving them doesn't actually stop in the city that they pass through. Instead they pollute the air and leave. Strong argument for taking them down, IMO.
But I've digressed. I agree there are challenges and never a one-size-fits-all solution. But there are solutions that are not currently being put into place that benefit the vast majority.
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As far as "Separated" I guess it becomes important to define separated. If there were physical curbs between, I could see it - but where I have seen that those tend to become even more pedestrian travelled, but even the flexible post at interval type ones, I've seen most of those destroyed in the first year they'd been put in by plows, UPS drivers, you name it. It's a bit of a tall ask to put in full on curbs, as much as I think it could work. Most of our major downtown streets aren't much wider than SF's smaller streets, with parking on both sides.