Some idea that flashed into my mind while I was discussing what rr will be in the new cIV. I liked it so much I made this thread. Pls comment! 
Make the railroad an instant transportation device like the airport. It should work only with connected cities and should not give any movement bonus other than the "teleport". Limit the number of units a city can RECEIVE per turn, make it improvable through different buildings (f.e. trainstation +1, marshaling yard +1, depot +2, cumulative) and have them cost more upkeep. This would be a neat capacity limitation, because I agree with the others that commented it is not a matter of speed but rather one of capacity. Also, it would make for interesting offensive strats (the disruption of the enemy rr-network by bombarding key points, trying to bombard those above mentioned city improvements) and defensive strats (defending those vulnerable points, unit placement for defensive action). It would also make it crucial to improve your cities on the border either as a defensive measure or as part of war preparations.
Keep the bonus for terrain like hammers and food. But make it dependant on the city size. Larger cities = more goods. so you don't have a bonus per terrain unit but a bonus of like one hammer per city population point. The map won't be crowded with those rr's anymore since they don't give you a bonus through terrain inside the city radius.
EDIT: Come to think of it, make the same capacity limitation for airports, but give them a higher number of units they can receive per turn from start on (like 3 instead of 1 for rr).

Make the railroad an instant transportation device like the airport. It should work only with connected cities and should not give any movement bonus other than the "teleport". Limit the number of units a city can RECEIVE per turn, make it improvable through different buildings (f.e. trainstation +1, marshaling yard +1, depot +2, cumulative) and have them cost more upkeep. This would be a neat capacity limitation, because I agree with the others that commented it is not a matter of speed but rather one of capacity. Also, it would make for interesting offensive strats (the disruption of the enemy rr-network by bombarding key points, trying to bombard those above mentioned city improvements) and defensive strats (defending those vulnerable points, unit placement for defensive action). It would also make it crucial to improve your cities on the border either as a defensive measure or as part of war preparations.
Keep the bonus for terrain like hammers and food. But make it dependant on the city size. Larger cities = more goods. so you don't have a bonus per terrain unit but a bonus of like one hammer per city population point. The map won't be crowded with those rr's anymore since they don't give you a bonus through terrain inside the city radius.
EDIT: Come to think of it, make the same capacity limitation for airports, but give them a higher number of units they can receive per turn from start on (like 3 instead of 1 for rr).