I don't see why this would be that hard to implement. I mean, I'm not saying it would be easy, but it could be done like caravans or something. For example, from a coastal city, you can purchase ships of various speeds. From there, you can "Board" your ship, then you'll be able to move across water as your boat. You can guard caravans (If Sea Pirates were to attack you, it would go to a combat screen involving the two ships locked to each other by a small boarding plank. You gotta admit, dueling a Pirate captain on the plank would be a very interesting thing.)
Also, why would cannons automatically mean peasants could use guns? Cannons for a long time were unwieldable by people on land because they were huge and unwieldy. Eventually, medieval scientists figured out a way to create handguns, but it wasn't until a good bit later. Firearms had been in use a long time before the renaissance, on ships and such. Even a few castles had some cannons.