The main issue is that the way zoning is done is really damn bad. Like not even American cities are that bad, zoning at its very very worst. There is no reason why it should be possible to have a much more flexible and powerful zoning code. Having mix use zoning, exclusion zones and so on. Why can offices and high density building not be in the same place?
I also dislike the roads, the basic building block is the road, but it should be the lane. You should be able to easily put together a few lanes, into a new road and then be able to use that. Currently you have to basically load 500 DLC road types just to cover all the basic things and even then it isn't great.
Parking, parking is the biggest problem with car based cities. And the game just ignores that issue, and that results in the problem with cars just being about optimization of intersections.
I also found the creation bus routes and other public traffic routes to difficult. It gets complex pretty quickly and once you have lots of them it just becomes almost unmanageable.