I'd like to comment further on this topic: as regards a transfer from an original iPad to an iPad II (my only experience so far).
I transferred purchases, sync'd, and backed up. Plugged in iPad II, attached to old account, restored from backup. Result:
1) Obnoxious but not crucial: all icons were rearranged.
2) Obnoxious: Flipboard (app) didn't have a record of my FB, Twitter, and Flickr accounts. I expected to need to log into them again, but not to have to create new links to them.
3) Troubling: All that was transferred were my apps. Now, I realize that I originally opted to transfer music and movies manually (because my desktop collection is rather large) -- but shouldn't what was on the iPad be part of what's recorded in the backup file?
4) Troubling: Considering the music, I took a look at the Capacity meter in iTunes (we'll ignore Audio, Video and Photos since I know what's up with those; manual transfer issue above). Old Apps: 6.2 GB, New Apps: 5.9 GB. Old "Other": .43 GB, New "Other": .39 GB. SO -- what's missing? I have no idea.
I'm not (exactly) complaining, I just want to warn others doing the same thing that it's not necessarily as painless as it seems to be made out. Be prepared for some road bumps such as these.