I think it has something to do with releasing chakra in pre set ways. You mold chakra and release it from your hands, then as you perform the hand seals the chakra gets mixed and moved in some set way, then add a little will power and poof you've got a jutsu. The act of performing the hand seal 'mixes' the chakra into the correct form so your mind can then work with it more easily. This is just a speculation though. I doubt it would be deemed important enough to explain hand seals this far into the story.