The problems comes the very first design decisions they made. The "Agent" system simply doesn't work especially in the way they implemented it.
Unlike better games of this type like the Tropico series those agents are not only carriers of resources, they are are carriers of information and they keep a persistent identity. SC's agents are only resource carriers, nothing more than coins in a soda machine using nothing more than gravity as their "AI". SC agents simply doesn't have an AI, it's a physics simulation using particles to simulate the flow of water when they should have been using a distribution function to do the job. The very core of the game is built on a flawed premise. Because of that this game will never be fixed.
Everything they have done was to cover up the fundamental design mistake they made at the beginning. The smaller city size was not a problem of not having enough computational power, it was a poor attempt to hide the fact the system doesn't work and came with a side benefit of enabling them to sell you DLC. They broke the RCI relationship because they couldn't get the agents to ship resources to the commercial zones. Nothing about the agent system works because they don't reserve any slots anywhere. Each agent is completely unaware of each other.
Those old games worked out well with the agent system because they assigned each agent with an identity and they were aware of each other so you didn't have half the town each morning racing to the first job they could see. They have a job and this is where they worked. They also did their best to find a home near their job. They didn't have traffic problems since everything was foot traffic, so the assumption was made that they could infinitely "stack". They also had needs so they would take breaks to tend to them filling in the rest of the economy like shopping and food.
The problems of SC run so deep they effectively have to make a new game to fix the issues.
Oh another smite! Is someones corporate masters not pleased and not trickling down? Still a temporarily embarrassed millionaire?