These are really two distinct wishes, but I've chosen to lump them together.
Firstly, I'm not a big fan of the way ships are upgraded right now. It is fiddly and feels quite game-y to me. I would split ports into two types; anchorages, and (uhhh) ports. Anchorages would be identified by little anchors on some coastal areas and would function much like our current ports (I suppose you could just use the same wharf graphic too). Ports would be coastal settlements with piers jutting out into the water. They could provide some income, but their major role would be shipbuilding. The number of ports controlled by a player would correspond to a specific ship type. So, if you control no ports, you get the crappy default ship, if you control many ports you get a much better ship. This has the advantage that a map-creator can decide how naval-y inclined each side is when designing a map (by giving that side access to more ports).
My second wish is towns. It would be nice to have a gold site that could be fortified and also serve as a vector point (perhaps only 1 or 2 vectors). It could be called a town, or a keep or whatever.