+1 to railroads, railyards, bridges, tunnels through mountains, etc - all tied to strat and resupply. Would be great to have valid interdiction targets in the game for behind the lines low level sweeps.
Also, and this may be more difficult to implement, but I would like terrains to have realistic routes for the trains - you shouldn't have RR tracks go up and over a steep mountain - instead they would have to skirt along the side of the mountain. That may require a change to be able to lay track at an angle to the ground; ie if the moutainside is a 30 degree slope, you'd need the ability to cant the track at 30 degrees to the ground to allow the train to remain upright.
It would look alot more realistic - as would RR track routes that run alongside rivers in valleys, across destroyable bridges, etc.