I too agree that this is a problem for the strategic game. Since patch 1.1, the AI is happily conducting naval invasions, and this brings the problem to the fore.

I'm currently playing a game as Milan, and fighting a war against Sicily over Sardinia and Corsica, and enemy armies are everywhere over the islands. Even though my fleet is vastly superior to the Sicilian, I cannot use it to prevent them reinforcing their invasions, or conducting new ones. Even sinking everything bearing the Sicilian banner, and blockading the port of Palermo, the Sicilians will simply build a single boat in that port, load it with a stack of troops, and sail straight through my blockade to land those troops near Cagliari, in a single move. Splitting my fleets up in smaller chunks is no solution, as the pirates or the French (Sicilian allies) would then take it apart with ease. The florins I paid to build that fleet now seem wasted. *sigh*