More rail options.
Have the ability to biuld anything from trollies/light rail, heavy rail (subways, el-trains, and on the ground), commuter rail (such as Chicago's METRA system) and high-speed intercity trains. They can keep monorails I guess, but I think they're kind of goofy.
Multiple main tracks with morning/afternoon fleeting. You could have 4 or more main tracks that would flow into the city for morning rush hour, and flow out for evening rush.
Have single tracks with sidings for lesser used lines and branch lines.
Have the ability to specify lines as being freight only, passenger only, or mixed use.
More station options!