Lol, why are you trying to find any logic in a video game, especially where story takes place in the future. And yeah, why not brain waves, even now it's possible to move, lets say a cursor with mind alone.
In the book it said something about a 'Brain up Display', or BUD. He also said stuff like looking at an icon to induce Stealth mode IIRC; and that blue objective marker, yeah, he has that too.
Not sure but I think the book mentioned something about hud display and eye movement. So yeah part galnce over that way, and part the onboard computer sort of predicts depending on the situation what your trying to do.