Some ideas on the train station:
allow players to place buildings at a start. provide a list of buildings available - player chooses which one to build/add at what point. Start with one or none and go from there. Keep the upgrades, but offer a little more personal flavoring options.
add a theater for movie viewing bonus
as mentioned in another post add a museum that can be leveled up for additional slots.
add a ticker tape on the concourse - ads?, news flashes?, competition announcements?
add caboose option railcar to maybe reduce maintenance?
add diner, sleeper, first class, second class, mail car options to increase passenger revenue and more train building options - like freight
have two tracks / single track sections on the map (eye candy graphics lol)
conductor workers to decrease passenger train wait times
charge a relocation fee to change cities
moving to HTML5 should enable you to produce some stunning graphics and a lot more bells and whistles