A question: what do people have against check-points? In a game like this, I think they are great as they allow you to play the game and not worry about saving all the time or trying to save every 10 secs to get that perfect run to beat a section.
Have you played Half-Life 2 or Portal? That's how saving should work, if you ask me. No worrying about checkpoints, and you rarely have to repeat bits with how well-integrated the autosave is.