When you connect to itunes stop the backup process by clicking on the gray/black little x to the right of the "backing up your ipad" on the address bar. After it stops, uncheck the box " automatically start itunes when this ipad is connected." Disconnect the ipad, then connect it again. If itunes asks you if you want to send error or crash reports to apple, say no.
Now you can press the sync button on the right hand side and see if that bypasses the backup process.
It might be a good idea to back up your itunes playlist to a usb drive or other external drive in case you need it in the future.
Your apps never disappear. Once you buy them from your account, you simply have to download it again. Of course the data from those apps disappear if you cant back them up
I agree that itunes is a pain to sync
