We've only played twice, both 4-player games. I can't speak for the folks I was playing with, but I definitely had to concentrate a little harder during the game to keep track of which cities were which type. I'm sure it will become less of an issue as I become familiar with the board. The part I found most difficult was when we came to scoring, and having to pick out the correct cities for each step. After the second game (should have thought of it earlier!) I realized that it will be much easier in scoring if we first remove all of the branchlets to reduce the visual clutter, then score the stations (since there are only two of them on the new board) and remove those tokens. Then scoring the cities should be easy.
Be careful; at least one of the new station master tiles award points based on where branchlets have been built.