I'm old fashioned and enjoy shifting so I prefer the manual. I don't think one is better than the other with these cars.
The auto box is excellent. Some people complain about the manual box being a bit clunky especially from 1st to 2nd, 2nd to 3rd. Mine was really clunky when I first got it but after diff oil and gear box oil change it's a lot smoother now, just a slight thud from 1st to 2nd.
The sport is only available in manual but S and SE models come with both transmissions :)