I mocked up what it would look like if everything for an entry was vertically centered: http://skitch.com/rrwhite/cm3m/reddit-centered-mod
I'm not sure yet whether I think that's an improvement :)
I think you should put the arrows to the left side, use simpler arrow graphics, and indicate the arrows are linked to the points by making them the same color. Then, make the 1, 2, 3 a lighter color that is there, but more in the background, and delineated in function. You also need to center them between the points and the left edge of the screen. They are slightly too far to the right to my eyes. This would meet your informational requirements while clearing the clutter that is harshing my zen. I think you should keep the change in the screenshot too. The balance is just so much better.