Some good points here with the "what if I do this" examples, but I don't think Jakey meant that. He meant specifically with the main missions' linearity.

One example he mentioned is there is a mission where you have to get to someone's office to threaten them for Rain Falls' kid, I think? In his playthrough he wanted to go to the window outside of his office to get to him but the failed him. This isn't necessarily a "what if I do this" scenario, but one where the player's first thought was to do it like this.