I kind of like the idea, for AI purposes, to have land units create their own transports (ala from Civ 5 from what I've heard). With that said, if the AI can be taught to do proper naval warfare, then allow the AI and players create warships which would allow some sea combat. As I see it, the mechanic of a land unit walking into a sea tile and creating a transport eliminates the needless micro of loading ships. It also allows the AI to consider all map squares for movement. On the other hand, the AI would need to be smart enough to make warships and patrol the seas. Have no idea how hard either would be to code but makes sense to me as a player.