I agree on point 2, especially the possibility to access railway stations from the two sides, integrate rail and bus station and build integrated passenger/cargo stations.
I also agree on point 4. It would give a much more dynamic gameplay. At present once the tracks are laid out there is little to do than replace vehicles (or maybe optimize routes to better employ the added speed*)
* I am not sure about this point, since I read that most destinations are set and do not dynamically change during the game (except when a location is destroyed) so that would not really alter profits (at least for passengers). Is that true ?