I haven't been playing that long, but I've gotten a house and started using the subway a bit, and it seems to me that it could be improved. I searched this forum, and only found the routing suggestion.
1. A way to specify what stop you're getting off at at the beginning of the trip, so that you don't have to be continually prompted to get off (or not). If you're on for a while, and trying to use the time to do cooking or something, it's kind of annoying and sometimes gets in the way.
2. The auto-router could use the subway in its calculations (if you have Your Papers, of course), and also work inside the subway (so it would say "Get off at Groddle Forest Junction" or whatever while on the subway, and if you haven't memorized all of the subway street names yet, you don't have to consult the map to find out when you're stop is coming up). A way to set the nearest subway station as your destination, without having to click around the map to find it first would be cool, too.
3. Maybe a way to prepay a bunch of subway tickets ahead of time for a reduced price, like you can IRL. Surely the bureaucrats could arrange this with some more waiting-room thumb-twiddling?