Sylar had been playing him the *whole* time (and possibly sleeping with him in Nathan's body? Was I the only one who went there?

You are *so not* the only one who went there. 'Cause I went Right There, too, right around the time when "Nathan" did the shoulder-clasp thing we've seen the real Nathan deploy to great slashy effect with Peter. And now, there I wallow, happily contemplating the creepy-wrong-hotness of it all... *eg*