I agree with you. I found that this felt more like they were trying to do a Sid Meier's Pirates! RPG (which is great, I love Pirates! Gold) and they had 90% of that done, then realized that they needed to shoehorn in the Watcher because it says Pillars of Eternity II Deadfire on the title, so they squeezed in the main plot.
But there is such a huge disconnect between that and the rest of the game, and it seems like not much effort was put into writing the main plot, that I feel like I would have preferred this as a Pirates! RPG set in Eora instead. Have a different main plot that factors into the powers in the Deadfire Archipelago, flesh out the faction system, make the sea more lively, get rid of the Watcher and have a privateer captain as the main character, and just call the game Deadfire: A Pillars of Eternity game. They have such a well crafted world (san retcons), that it would be a waste to just have it focus on the Watcher whose story arc already ended in the first game. His reason for being here is... well not that great really but you should finish the game first. I loved the game, would have wished more polish to the ship aspect (pirates attacking other factions and not just you, trading, working politics, maybe just make the ship battles be like regular battles except the player is a ship with a class and skills like fire broadside/port and jibe, etc), but found the main quest to be the weakest part of the game.