I was adding that I made the mistake of passing through Times Square on my way to some destination a number of months back. As in the article, you literally could not walk on the sidewalk which was effectively blocked by the mass of people. Times Square (like areas of downtown) is an extreme example, but things do get really crowded. (And you can't just do away with road traffic there. You're at intersection of two major N-S avenues.)
Ideally, streets would be used only by pedestrians, but I acknowledge that's not feasible.
They are one way. Almost the whole of Manhattan is.
Broadway is already narrow. Seventh not so much, but car traffic there can frequently be as bad as foot traffic. I'm not sure what a good answer would be.
Add second floor above the road. And on top of it, a third floor.
Like an expressway? What about exits, turn-offs, on-ramps? Where would the city find the land to build these?
Most vehicles driving around Times Square are at least fairly local; they're not looking to bypass Midtown Manhattan. If they wanted to, they would probably have driven the short distance to FDR Drive or the West Side Highway.
(Literal plexiglass cieling)
Pedestrians
Bikes (if not with pedestrians)
Transit vehicles (in what is now a service tunnel/grid)
Yes, this would actually require ventilation engineering, but a city should anyway. You might also push for highly restricted emissions vehicles. CNG, Hydrogen, and Electric come to mind as things to consider for a white-list.
You'd have to fight a lot of business owners. Most transit in Manhattan is by foot, and you will have separated pedestrians from commercial entryways. As it stands, a great deal of storefronts—even in the most commercial and highly trafficked parts of the city—are in mixed-use buildings, with apartments in the upper stories. Now most potential customers, instead of walking past shop after shop, are walking past residences. Signs may point out what lies below. Presumably this would cut into businesses which rely on customers popping in without planning to; if you weren't going to exit onto that block for something else anyway, why make the climb down to commercial level just for a little something that caught your eye?
And how did it catch your eye? Stores could no longer entice with a storefront, by showing off their inventory and sales. Restaurants, bakeries, and coffee shops could no longer waft out onto potential guests. They'd be in virtual basements, and would be much less attractive for that reason alone. Manhattan has a history of severing its residents from one thing or another—waterfronts are the first to come to mind—but I would be surprised to see them do this.
Of course, not everything has to remain as is and the city may evolve (as it has before), but this sort of plan would require much more work than building a tiered roadway.
Maybe in the future, when 'brick and mortar' starts to fail even in densely populated areas, the problems described above won't be problems anymore. But then, neither would the traffic; and the tiered roadway would be redundant, and not worth the money to maintain (nor the daylight lost).
There are walled-off backyards and "gardens" within big blocks. Just make them open
For most blocks where unloading is a problem, courtyards are narrow, uneven spaces that frequently do not run the length of the 'interior' block.
The city would also have to justify reclaiming two lots per block—on either end of the courtyard/alleyway—in a city which already has a housing shortage.
What's the difference?