Much of this has been mentioned, but here is what I'd like to see:
-No more depot requirement at beginning and end of line
-Ability for railed transport vehicles to reverse at terminus stations
-More control over city building/growth. Don't mean this game should be the next Sim City, but it would be nice to have a greater control over where buildings pop up, and what kind.
-Greater modability, building packs should be something that the modding community can create!
-Customizable paint colours on vehicles, giving our transit fleet its own unique look