This is trivial, but I've noticed that some of the ports don't really reflect the actual historical port. In some cases the work the devs have done is really impressive -- Sansbury, GA no longer exists, you'd only find out about that if you did major historical work -- but then conversely, the port of Charleston is just all kinds of wrong. It's not even on a peninsula!
Thing is, for at least some of these ports, there actually are period drawings, too, so the game could model them for "accuracy." (see, e.g., http://i.imgur.com/TZSMHfW.jpg for a roughly 1820's portrayal of Charleston Harbor).
This is of course trivial and should probably be the lowest priority imaginable, but it would be nice if they had the art etc. resources and time for it.