Here's my thoughts:
1) Rail and Highways: I don't care if I can build the stations. I would like to be able to construct a rail route much more quickly without unlocking everything from the start. It should be, at the least, when you start, so you can at least get the Rail > Metro > Bus/Taxi thing going on early in your planning which means you don't have to bisect a bunch of high-value built-up land from the start. The same goes for highways. It doesn't make sense from a planning perspective. In SC you had to wait for it to be invented. That doesn't apply here. Building a rail network, even without stations, should allow for a much smoother transition into pods of smaller towns or huge city, district-by-district transportation.
2) Make money matter: It really doesn't. It's almost an afterthought after you break 10K population. Really. It's too easy in a lot of ways. Add some additional challenge here. Which also plays into my next point:
3) Add more building level control of the budget and have the radii actually reflect the true area of impact. Rush Hour did this really well: One high school may need the ability to accommodate 2000 students. Another may only need to cater to 250. This needs to have a slider for these buildings. This should apply to all service buildings.
4) Traffic Pollution: This is a big one. This needs added. It is hugely important to the realism level of the game. Right now, there's no drawback for eschewing all mass transit and simply building tunnel networks to bypass all that overhead and expedite rides. There also needs to be an option for Heavy Transport only on certain routes. Potential congestion charges and tolls should be rolled into the game. As well as "green initiatives" like electric car initiatives that require you to waste land on charging stations to support the infrastructure (part of the tradeoff.)
5) Tourism, the Airport, the Passenger Harbor, and Unique Buildings: Simply put, this has no correlation to the size of your city. Las Vegas, is, for all intents and purposes, not a very large city. Yet, it regularly hosts events that will quadruple the size of its population. I read about some "agent limit" or something that seems to detract from this since the AI goes haywire or something. But this should be a long-term goal. Then to go a step further, allow for special events (games at the stadium, big trade shows at the Expo Center) that will be tied to an attractiveness index that opens up what you can book. Now this is really in depth, but it really should have been what After Dark should have included. This really opens up a great metagame that these massive influxes will really put your transport system to the test. Get creative with each of your unique buildings, then add this stuff to the asset creator. Tourism needs a good hard look taken at it overall.
6) Parking Garages: Parking Garages need to be baseline and function similarly to schools or police departments, facilitating a larger or smaller area based upon funding.
7) Passenger Train Stations and Schools: In addition to building level control of range of function via building-budget sliders, these need multiple sizes. Elementary schools and passenger train stations need small, medium, and large sizes. High Schools, may need medium and large. Large Passenger Rail Stations need to facilitate multiple incoming and outgoing rail lines, just like in every major city everywhere. Additionally, there needs to be an underground option for this. Penn Station in NYC comes to mind.
8) Media: TV Stations, News, Radio, potentially Internet: These need to be facilitated. There's dedication via tax incentives everywhere to allow for this type of development. The game should allow for this via Commercial Specializations. And I'd wager that Retail should have its own specialization, as well. It's somewhat humorous that I start a new town and I end up without a Supermarket due to the randomness of development. What are they eating? Dirt?
9) Rail Line designation and, to a point, Design: Rail Only/Passenger only. This could probably be done relatively easily. Rail also isn't one way. A train may come in on a rail, then go out on the same rail, which hurts the detail of what rail is. The switch can be down the line. We need to have the ability to add the switches. It should not be automatic. The Metro is a train, too. It should likewise offer that. Additionally, allow for higher speed rail. HST's, potentially Mag-Levs, would be amazing!
10) Idiocy does not equal Industry: This sucks. It really does. High-tech industry is tied to high-end engineering, who are some of the most educated people on Earth. Even Miners, Oil, Farmers, and timber can involve the super-highly-educated. This really needs some work. Additionally, you need larger models for Timber and Farming especially. A farm should have the ability to stretch out to massive sizes and provide tons of produce. If you really want to get nuts, designate Organic and Non-Organic areas which increase sales prices, but lower production.
11) Open Space, Forests, and Natural Beauty: This isn't factored anywhere but Land Value. Put in a Ranger Station or Camp Ground. Put in a District tool for reserved Natural Parks or something like that then add Mount Rushmore and other such Natural Monuments.
12) Preference: Cim preference in where they work or live cannot be controlled. They will on a whim, work 4 tiles from where they live with somebody commuting the exact opposite direction FOR THE SAME EXACT COMPANY. The AI needs some work in this regard. It yields tons of unneeded traffic and commuting.
13) Police: Police are far too efficient. There's no crime. They need tuned down.
14) Time: If it took me a week to get home from work, I probably wouldn't work there. The time system is really weird. 7 days of sun, 7 days of night. I don't really get it.
15) Arcologies: Now I personally can find these insane, but simultaneously, it could be a means of saving land and consolidating your property and getting around that agent limit. City-in-a-building could theoretically reduce the loads on the framework to avoid any and all issues that may be limiting the introduction of a more robust tourism system.
Which I'll hold off from there. Like I said, I love the game, but having hit my first city at 250K Cims, it's really a shame that I can ignore everything and just zone ad nauseum providing services where needed, providing cross-town tunnels or bridges, and ignoring all mass transit, since the overhead associated with unique buildings, tourism, and mass transit is simply overshadowed by oversizing your road network. I think there's a lot of things this game does well. It's gorgeous, the base game is spectacular, and the ideas are sound, but while Rush Hour had its own bugs and problems, this game simply falls short in a way of many of its features. It needs a bit more depth.