One thing I was hoping for was a better way to name things in your city. SC2000 had lame little signs that you could put up, but even these have been eliminated. Simcities are anonymous cities, whose neighborhoods, streets and rivers have no names, alas. The biggest disappointment of all is that they really didn't change any of the transportation elements. The streets and train tracks look better than before, but they work exactly as they always did.
Bridges can exist only over bodies of water, and only at sea level.
In real cities, roads, train tracks or whatever need to be able to cross each other in any combination, at any level and any angle. Train buffs like me would have liked to see some more rail options, like narrow-guage lines, street trams, elevated trains, or even futuristic monorails. Another beef with Simcity is that it has no international or historical context. Simcities are 20th-century American cities. This is ironic, as to my mind, the most interesting cities are to be found in Europe.