1) Slighty more varied zoning. For example, either the ability to zone specifically rowhomes, or removing single family dwellings from medium or dense residential. The ability to zone or influence zone developement. Like zone with height restricts/favoring. You might designate high density commercial or residential to be skyscraper preferred. This might work, or might backfire and not build anything if theres no market.
2) More varied LARGE parks/plazas, with multiple graphics for 2x2, 3x3, and at least 4x4. Possibly 5x5 and 6x6. Also, the ability to zone parks. In large areas, they would work much like agricultural industrial. The entire area would develop (and cost much like individula parks) with a semi random patten of grass/trees/water/paths.
3) Even more bridges, I love the new pickable bridge system, but in reality I would like even more choices. Mainly a few different graphics for each base type. Like stone arch would have 3 different looks. Steel arch might have a few different looks/colors.
4) Diagonal bridges. Possibly diagonal ports and ferry terminals.
5) Diagonal plots. For example if you were to zone a corner with a 3x1,a 2x1, and a 1x1 next to each other, they could combine into a trangle 3x3x3, and develop a building such as a Flatiron clone.
6) Maybe a system where the roads are a bit wider, and incorporate a built in sidewalk that can be built on. Subway stations, bus stops, trees, benches, public art, etc. could be added onto the road tile itself, showing up on that sidewalk. I know current streets have a sidewalk, but its not the same. (example- A subway stop would be under the roadtile. Above ground, stairs would show on both sides of the street. If placed in a road crossing square, the station may have stops on all four corners.)
7) Even more transit systems. (I love Rush hour!) These would include Streetcars/cablecars. 2tile wide roads (like avenues) which include trolley tracks down the center (looping at the end if not connected). The streetcars would travel these tracks, increasing their capacity. This however would be at a limited car capacity. Overall, they would be like avenues, but with instread of the larger car capacity, they would retain the normal roads capacity, and the extra passengers would take the trolley. If the car traffic can't find other routes, and becomes to great, both services would suffer. I would also like to see elevated rail thats over the street as well. But I can live with out it.
8) Modifications to the subway system. If you upgrade your normal subway line to double wide (or high capacity) you can then designate or upgrade subway stops to be express stops. This would increase(maybe double) the capacity of the stop, and remove alot of congestion. Express stops couldn't be placed on basic lines.
9) Aerial trams over water, or up/across steep terrain.
10) Rewards with multiple graphics. Like City Hall. When placed, you would be prompted to pick one of a few graphics, allowing you to customize your city a bit more. This would include things like Arenas/stadiums, etc. as well.
11) The ability to "zone" historical, dragging it over sections, or at least entire blocks. I would like to see the no-bulldozer option to historical buildings returned. I don't know why they removed it, but I would like it back. (maybe a second checkbox under historical)
12) Larger(numbers wise) building sets. I know they increase the system requirements, so maybe you could have the option when building a region. You could choose normal building set, large, and huge. Huge building set would be very demanding, but give your city a much more realistic look, with 2 or 3 times the building types of normal.
13) More varied terrain. Like SC3, colored terrain denoting different climates. And trees. I do not like palm trees, and it bugs the hell out of me every city I build is filled with them. I can understand the Houston set...but Chicago and NY? WTF?
14) The ability (probally is a add on or stand alone companion program) to walk/fly/drive through my cities. The city wouldn't be playabe in this form, but you could see skyline views, street views etc.
I got more, but I need some lunch. Heh.