I voted for Jolly Roger as well, mainly because of the fact that he's the main enemy in the game, which with how the story is going at the moment, doesn't look like it's going to change for a while.
Ravens Cove as an entire chapter would be too limited, because it only revolves around one place, with only a section of the lore to boot.
Davy Jones/The Kraken would be the same as RC; too limited. The only place that Jones has under his control is Isla Tormenta, which is filled with very high leveled enemies. That being said, right off the bat, it would make it difficult for the average pirate to hop from one chapter to another, because most finish their story quest in the mid to upper 20's, while your then be sent out for 15 gills from Thrall Captains. Also, what exactly is the hype about that darn squid in the first place? If anything, it'll be a 5 to 10 minute battle where you have to use cannons to shoot at it's tentacles, and the occasional slashing and hacking of a sword. Guaranteed, a week after it's release (if it even is,) people will figure out the pattern, beat it repeatedly, even solo it, and then get bored.
Lord Beckett and EITC would be doable, but I would think that Jolly Roger, being the almighty socrerer of the dead and such, would have a wider story range. Beckett and his army, being bound by mortal chains, really wouldn't have that much gusto against what Roger could do with his imagination.
Rum... I think I'll need to "test the rum" out before I make that judgement
New weapons and enemies should be
included in the story chapter, but by no means should it revolve around it. Building up all of this tension, with the island destruction, the invasions, the GM events, it would be a let-down to see a story chapter that wouldn't involve taking the fight to the enemy, for the sake of taking the fight to the enemy.