If you install Gnome Color Chooser you can select 'compact profile' which is a global setting for padding. It shrinks all of your buttons and other white space without you having to edit the theme by hand:
BTW I have always hand tweaked the font, DPI, and all appearance based settings on a fresh install of any GNOME based distro. I am not enraged on the padding issue, but it would be still nice to see optimal configuration out of box.
sudo apt-get install gnome-color-chooser
Find it in System→Prefs menu after install