I think that being able to pick your side would be interesting. However, unless they did something like Races (in other mmos) that you'd pick at the start, each with different starting areas. Now, considering this be a pirates game I would not suggest my idea, and neither would many, but it does sound like an interesting start to something big
But, there could be quests (as said many times before) that allow you to disguise yourself as all of the groups of enemies, in order to complete quests and earn notoriety as said enemy group. THAT would be a fun one. A seperate island or two for Davy Jones, EITC, NAVY, and Jolly. The quests would be to help pirate-folk retrieve certain items from their home bases and maybe sabatoge plans that Davy Jones has made. All of these would require a costume, of course. You would earn these from other main character quests (quests from elizabeth, jack, barbossa, etc...)
P.S. - could ye ellaborate on what you mean when you say reply cutscene? thanks