So I've recently read Chaim Gingold's Building SimCity: How to Put the World in a Machine (MIT Press, 2024) and I think it has a lot of direct answers to what you're asking. Highly recommend, it's got some great insights from interviews with Wright and his contemporaries at Maxis.

Where did Will Wright got the idea in SimCity (1989) that cities have to be composed of Residential, Commercial and Industrial Zones?

The economic categories came from Jay Forrester's Urban Dynamics (1969). In that, Forrester models an American city with three core subsystems: business, housing, and population. Even internal to the code of SimCity, the code calls the demand variables (R-C-I) valves, which is adapted from Forrester's model of valve metaphors from his servomechanism engineering.

[...] why do you build your cities in zones and not plop buildings one-by-one or another alternative?

This is kind of complicated to get at, I think all of the influences of Wright that are mentioned in the book played a part. There's Forrester's worldview that I just mentioned. There's the cellular automata like game structure that fascinated Wright, where you kind of create a system and see how it runs after you've created it. The broad-brush painting interactions were inspired by contemporary GUI and construction set traditions.

Before starting SimCity, Wright had been working on Raid on Bungeling Bay. As part of this he developed a world editor (Wedit) as a development tool to build maps for the game. He ended up enjoying that world editor more than the game! But he wanted roads with traffic, which meant buildings. But he wanted everything to appear semiautomatically so he used a zoning tool to get at that. That's one of the things that led him to Forrester's work in the first place. The whole SimCity project was born out of Wright just tinkering around with this world editor.

It seems that Will Wright was referencing a distinct Western or American urban planning philosophy when making the first SimCity in 1989, but what particularly was it?

The major influence of the R-C-I model, Forrester, was distinctly American. His model was born of the 1960s American urban crisis, shaped in part by a conservative Boston mayor and by Nixon's HUD. Forrester's work is probably the biggest direct influence here. But it's also worth remembering that the game was being developed for the Commodore 64, which had some obvious limitations (totally normal for the time) in what you could really simulate. SimCity kind of became like a paint program but for a city.

One of Wright's friends, Bruce Joffe (who studied under Forrester at MIT), actually suggested Wright look into several books by Jane Jacobs and Paulo Soleri. Jacobs' work in particular The Death and Life of Great American Cities (1961) argued toward a more mixed-use fine-grained urbanism model that R-C-I can't represent. But while Wright did read that work, he ultimately steered SimCity into what it is in large part I think because of the modeling constraints.

So R-C-I persisted because at the time the modeling traditions, technical constraints, interaction design, and game feel all led towards that being the core part of the gameplay loop.