Few more things:
Easier vehicle upgrades. Click on train, push the “Upgrade” button, select locomotive/cars, and then have an option to only upgrade this particular set of the entire line.
“Snapping” stations. When you build a new station next to another, you can snap the new one to the old, just like the double/triple/n-tracks work. Not a biggy, but certainly would help the people with OCD :D.
I think Mansen and jm mentioned these things in their vids as well.