I’ve got some additions to your list:
-A pop-up or warning when one of your vehicles hasn’t moved for more than x months/years, because they’re stuck in traffic/get blocked by other trains/are waiting for a bus blocking a stop because you accidentally selected ‘Full Load’ for that stop.
-Underground/elevated train(/tram/metro) stations.
-Dedicated (working) bus-/tram-lanes to bypass traffic jams.
-A fix to the popup windows so they’re not appearing allover the screen and/or partially behind menu bars.
-A minimap
-Train priority selection.
-Animated signals
-Suspension bridges
-Viaducts (for those elevated railways) and those cut-out below street level sections with straight brick walls (don’t know the proper English term for it, but they’re the opposite of viaducts, like a canal).