Thanks to awesomeadvisor787, I learned about the Simtropolis Network Addon Mod (NAM) for SimCity 4 Deluxe or SimCity 4 with the Rush Hour expansion pack. While I haven't tried everything in it yet, I have tried the some of the features and while it fixes some things, some options also take some of the realism out of the game.
When I first installed NAM I choose the "Radical Custom Special" option for my "traffic plugin." This traffic plugin both greatly improves SimCity's pathfinding heuristics and increases the load capacity of the different network options (e.g. subway lines). I played one of my cities for several hours using this plugin and found that it greatly diminished game play because it took away all of the challenge of managing traffic thus removing some of the realism.
I uninstalled NAM and then reinstalled it choosing the "Perfect Pathfinding" option for the traffic plugin. Anyone who has looked at the routes Sims take using a unmodified version of SimCity knows that the commuting routes taken can sometimes be really stupid. Perfect Pathfinding resolves this issue by helping to ensure Sims actually take the most efficent routes from point A to point B. I really like the Perfect Pathfinding option because a real person would tend to try and take the shortest/fastest route for their daily commute, thus it improves the realism of the game. Also because Sims are taking smarter routes overall traffic loads are significantly decreased as is average commute times. When using Perfect Pathfinding be fore warned, it does greatly increase the processing and calculations SimCity has to do for a city, which can have a detrimental impact on game performance causing freezes and game studder. To avoid this problem on slower systems, I might recommend choosing the "Better Pathfinding" option instead.
Another plugin that is part of NAM that I really like are the turning lanes for roads and Avenues. Like in the real world, adding turning lanes greatly helps improve traffic flow at intersections. Once this plugin is installed all one needs to do to retrofit in the turn lanes is to select the appropriate road/avenue type and set a road/avenue tile in the center of each intersection.
I do have two gripes with the turning lane plugins. The first complaint is that it does not work on intersections with mixed road types (e.g. a road intersecting an avenue) and with U-Drive missions the player driven vehicle has a quirk that causes it to always go into the left hand turn lane at intersections regardless of whether the vehicle is going straight or turning (either to left or right). This bug frequently causes unnecessary crashes during driving missions. Computer driven vehicles don't seem to have this problem. I really wish these two quirks could be fixed.