TLoU succeeded as much as it did because of its storyline. Narrative Director Neil Druckmann beautifully guided these two characters on an incredible journey that always went a particular direction that would always end with the fateful scene we all know today.
Changing the way in which we engage with the characters with a choice based system in The Last of Us Part II certainly would give the player more control over the story. However, within the universe of TLoU, a choice based system in which the choices we as players make alters which storyline we follow will not benefit the game itself.
The ending of the original game was so polarizing because there was no other option. The story always ended in the same exact way, no matter how many hours you put into the game or how many infected you did or did not kill. Each player gets the same experience in terms of the story. If The Last of Us Part II deviates from the single story track, it could create a disparate experience for their players and distract from the story they really want to tell.
Part II should allow players to fully explore and experience a well thought out story that knows what it wants to say and where it wants to take us.