Several large cities in China that I've been to tend to use pedestrian tunnels at many large intersections. It works pretty well - subway-like staircases at each corner, and nice wide hallway/tunnels going around the whole intersection. Occasionally with some shops.
It has the advantage of being easy on the eyes above-ground. I can imagine in places with serious homelessness issues there could be problems, but the ones I experienced were fairly nice - some more plain than others, but generally graffiti free, well lit, and well used.
If you are disabled (permanently or temporarily), old, have strollers or luggage, then level-changes add quite some time in the best case or are completely unusable in the worst case.
In my experiences traveling with Asia, usually these systems were not outfitted with elevators.
Harvard Square has this, by happenstance. There are entrances to the T on both sides of Mass Ave. and you don't have to go through the turnstile to cross from one to the other.
In downtown SF, you could put lower diagonal street bridges which would save an infinite amount of time for people driving.