Density can be miserable, but San Francisco is far away from the levels at which it becomes miserable. Midtown Manhattan is probably approaching 100,000 people per square mile, but it seems much denser than that because Manhattan more than doubles in size during the day so the daytime density is probably approaching 200,000 people per square mile (for reference, china town in SF has a nighttime density of 75,000 per square mile).

100,000 per square mile is not at all miserably crowded. I was working here right after Hurricane Sandy when all the commuters were staying home, and it was not crowded at all. My neighborhood in Chicago, which is probably around 50,000 nighttime density, feels positively empty on the weekends.

You could double the density of most parts of San Francisco and still not even be approaching "uncomfortably dense" (that would take the CBD to ~100,000 and areas like the mission to ~50,000).