It most definitely picks up a couple of mpg as it breaks in. I do a lot of freeway driving, and I get consistenly 23-24 mpg (after break-in). I have the 6 speed. If you really baby it, you can get over 30, but I suspect it is fairly hard to do.
I don't think anyone has proved, without a doubt, of whether the manual gets better or worse mpg than the auto. Too many variables, I suppose.
My album has detailed info on the mpg I observed in the first 8000 miles. I was very carful in my calcs. This info was taken in the super heat of Arizona, with the a/c on 100% of the time, dragging down my mpg by about 1.