Another alternative would be to run the game as a couple of lone wolves. That way you have 3x guaranteed new quest content.
Basically whatever origin companion you are not playing as your main character will give you a quest line you can follow. It's essentially what you would go through if you had picked that companion to play as your main, except that you have less control over how they will act. That means, as you surmise correctly, that if you want to keep some stories fresh, you had better pick 'faceless' mercenaries or indeed go lone wolf.
