it would be much much better than chase eothas. It would the game's biggest problem that's sense of urgency when actually your fucking around the island.
The only correct answer to the story of Deadfire is completely annihilating the gods and ending their tyranny over mortals, because they are fake gods. They are not the absolute power as god is conceptualized to be in real world. The struggle they portrayed in Deadfire was imo completely nonsensical and stupid after the revelation in the first game that the gods are phony constructs made by humans. IMO how they should've branched the story is like this:
Either the watcher,
1. Completely destroys the gods - AKA Prophetic liberator, destroyer of idols ala Moses.
2. Rules over them - AKA Strict materialist industrialist
3. Gets in cahoots with them as a partner - Theocratic Sovereign
They came up with this excellent setup in the first game which could've been developed into a fantastic mirror of mankind's ascendance out of the dark ages, but they completely lost the thread in Deadfire. They chose to operate within the pantheon of the gods as if they are absolute powers (which they really are not as much as they seem, since their powers are by design, finite), when instead they should have superseded it with the watcher raising above the gods. It's a game i play for the RTwP, as opposed to the first game which really excites my imagination.
They could've tie in the factions in nicely too, as one could work to achieve one of those endings. For example, the scientific Vailians could've helped ruling over the gods through scientific mastery - which they even endeavor to in the game.