I am not sure if this is a good idea,but when I get too frustrated and don't need to backup my iPad,I use a software called Backoff which turns off the auto backup function of iTunes temporarily,saving me from hour long backups,hence that decreases the time for a complete sync process,but this isn't recommended. In my experience when you uninstall iTunes nothing gets deleted in your iTunes library(I am not so sure but in my case my library remains intact when I uninstall iTunes and install updates or some weird reason downgrade to older versions). But you know I am not even saying this. Btw,back off when used to turn off the backup the iTunes will launch in install mode,that is it will seem like it's getting reinstalled by itself but nothing of that sort happens literally,it'll show that preparing to install thingy and then launch the iTunes without anything changed. This reinstall thingy happens only once. You'll need the .net frame work 2 to run back off for windows. Once again this is just an information that might help by reducing the huge auto backup process time waste(when you don't need it),and only use it if you are feeling over adventurous.
P.S: This only disables the auto backup that happens before the sync process,but if you want to backup you can do it manually but right clicking the iPad in itunes and selecting backup.