It would not shock me if some sort of prologue is added upon the full release of the game.
I wasn't part of D:OS2 Early Access - but from what I recall you didn't start out on the ship in that game's Early Access, you started out on the beach. They added in the ship at full release.
I also agree the game would benefit from a prologue where you meet some of the companions before the ship, meet some of them on the ship when you are plucked up, etc.
With the expensive CGI cinematics, I doubt they will get rid of it - but maybe? For example unless Karlach backstory changes if she is picked as Origins (assuming she is companion/origin character) then the cutscene doesn't really fit her, as the ship goes to hells after infecting PC... How and when she got tadpoled, with ship being under siege always felt weird to me to begin with.
I am not sure what prologue Larian could add that wouldn't be contrived - the capture is the meeting point for our heroes, before that they have different objectives, and from what I understand were captured in different places.
That said, I will be surprised if, at the very least, the ship itself won't receive a revision, once all companions and all mechanics are set in place.
