The following info and commentary comes from Jean-Sébastien Décant, lead designer...

On JRPG-style naval battles

"We also have the Kenway’s Fleet mini game where you can send ships captured in the open world on trading missions around the globe. It also features a JRPG style naval battles mini game to secure trading routes and avoid losing ships to other pirates. The Kenway’s Fleet mini game is part of the companion game offer, meaning that you will be able to access it from the captain’s cabin on the player’s ship in the main game but also from a smartphone or a tablet."

The following info comes from game designer Tim Browne...

On multiplayer naval battles being considered

"There's a couple of things [keeping us from doing this]. It took the Shanghai studio three years for AC: III just to do the [campaign's] water physics, which gives you an idea of how much [effort] it took the team to do. To then replicate that seven more times is currently a technical impossibility. But we did consider it from one point of view...lets look at the DNA of Assassin's Creed multiplayer. Is it about being the captain of a ship? No, it's not. It's about being a badass assassin, being the best assassin out there."

You can also hear an audio interview with Mr. Browne in the player below.