If you could rebuild a city from scratch

This is a rather poor proposal. I mean it doesn't even attempt a modicum of non-bias as it doesn't even include a "disadvantages" section, which most notably holds: any leak in the membrane between soil and concrete can significantly reduce the longevity of the roofing structure, meaning property managers will inevitably be facing leakages below the top level - thus meaning the property managers would face significant problems attracting doctors offices, medical clinics and even food services places as any serious leak would be cause for closure and could incur serious expense for the property owner when they'll inevitably have to pay for lost income.

While I think this is a great idea, I'm doubtful that the advantages significantly outweigh the disadvantages.

Another notable disadvantage is that if you plan on growing anything more than grass and flowers AKA a tree, you're going to need significant soil depth in areas. This means that the building is going to have to cope with not only soil weight but of the soil becoming super-saturated with water. The drainage of the soil so as to avert too much water sitting in the soil. So on and so forth. Adding hundreds of tons of soil and water onto the roof of your building is going to put excessive demands in place and sky-rocket construction costs in your urban core. Given that many cities have a problem keeping businesses in their urban core, I don't see how making it more expensive for them would be beneficial.

Speaking of earthquakes... How would an entire city react when it's tied together like on giant building? My guess is the legal aspects alone of determining cause of damage would prevent this type of city-wide design.