An urbanism focussed city builder where you start with an existing city in the current car-centric style, possibly including a couple of dozen kilometers around the city so rural problems are included as well and have to transform it, with realistic building project times, into one that is more walkable, has safe bike paths, good public transport,...
In particular I would also like it to take verticality in to account both for transport (people and bikes and trains have a harder time going up and down than cars, boats need locks,...) and for buildings (stores at the bottom of a building, residential above,...) and that accounts for the huge amounts of space car-centric cities waste on parking as well as the ongoing infrastructure costs for maintenance and replacements of all that infrastructure in sprawling cities.
Sadly nothing so far. Most city builders for modern cities tend to use the sim city simplistic zoning model, ignore verticality and building is super-fast and stuff does not have maintenance costs once built. They also mostly focus on cars and mass transit, not so much walking and biking.