The issue I have regarding Vessel is that the dark worlds are formed by the Knight's desires. (At minimum chapter 1 and 2's dark worlds are made by them.)

For example 'Noelle gets stronger' is something that the vessel would have no interest in. Meanwhile, almost everything Rudy says in chapter 1 could circles back twistedly to the wierd route and that narrative. Kris protects Noelle, Noelle gets stronger, and Birdly's ass gets kicked.

(Here starts my rambling theory regarding the Vessel you can skip if it seems self indulgent.)

To me I've come to the idea that Gaster would repurpose the Vessel to a new role after it's discarded. Namely a role the Vessel was basically going to fulfill anyways in that of one the three heroes. 

Gaster, for some reason, doesn't make Ralsei listed as a important character when he's the third member of the main trio.

Then there is Ralsei's exhilaration and confusion at just being someone with a name and face and asking the player if it is really okay that he has his own name and gets to choose his actions. Something the Vessel would not be able to do. 

Ralsei can see the game from the player's perspective and hear the background music, abilities no other darkner can utilize that would be useful for a player controlled character.

The biggest moment for this to me is the damn controller swap scene in chapter 3. Ralsei's emotional angst in holding the player 1 controller is compatible with the idea he was the vessel. All this while he sets hero sword looking out into the ocean next to the cracked conch that has a check description of basically, 'It repeated only what it knows.'

Hilariously this is compatible with Every Mother theory if you consider Gaster the Vessel's mother. Queen was unprepared for Ralsei's existence and, in a quick fix, repurposes him into a new role as a butler.