Right now (as of beta 3) ports are the only junctions (for non-flyers) that connect land and water. Normal coastline is an impassable barrier. I think it would be more interesting if there were two types of coastline..lets call them beaches and cliffs.
A cliff would act exactly the same as the current coastline, you could sail along it, but only fliers could move from a cliff square to a land square.
A beach would be like a one-way port. Boats could 'beach' themselves there, meaning they could enter a land hex from a beach. However, a unit walking around on land would not be able to move onto a beach.
This would give mapmakers some options. If you wanted a coastal city to be vulnerable to sea raiders, you could put a beach next to it. If you wanted it to be safe from seaborne attack, surround it with cliffs.
If swimming units do get introduced, perhaps they could use beaches like ports.