DutchCourage
Chieftain
If you have more than 2-3 cities, moving goods around in wagon trains and ships soon becomes tedious. Trade routes don't help much either.
I think you're actually mentioning the single biggest improvement - possibly the only one.
The only reason I bought the game is because of my miserable failures in getting the old game to run on new computers. It is definitely different than Col I. I for one enjoy the challenge, you have to start thinking strategically from the get go or defeat is a certainty.
Oh, and for those comparing things to Civ - stop please, entirely different game.