Cars are dangerous and the best engineering solution is to isolate pedestrian scale speed and mass transfer from multi-ton industrial equipment. So go 3D, give cars their own isolated layer, give pedestrians and slightly faster moving exposed humans their own layer.
On a side-note, I was in Boston this summer and it's so much more of an airy and accommodating place than I remember from 10-15 years ago. Lot's of the COVID traffic calming and patios still in place. Awesome, go Boston!
I'm split between an idea like Tokyo's underground mall areas (which work really well with climate control) and just over-specing several stories above ground for a platform layer that can be level across the whole city and completely free of non-emergency moving vehicles.