The naval combat was definitely awkwardly tied into AC3. It felt like they were probably debuting it then to get some feedback from gamers while developing AC4 in the background. No idea if that's true, but it seems likely enough.
There were a couple mandatory missions that forced it on you and then after that, going sailing was an optional thing. I wouldn't say that any of it was mechanically bad, but it was really boring. It seemed like it should be something that was really grandiose and fun, but in reality it was a chore.
Of course, I really wasn't enamored with the sailing in Wind Waker either, so it might just be a game mechanic that doesn't work for me. The sense of discovery there kept it interesting enough to keep me playing, but in AC3 it was just a mission-based affair so it had none of that much needed flair.
