Usually, if your iPad has been jail broken in the past, it's easiest/best to use the "download the firmware and upgrade via iTunes using the shift key" process. The iPad is put into DFU mode beforehand and then the process is started.
If not jailbroken, it's six of one, half dozen of the other. Mainly, people use that method because they find it easier to get the IPSW (the version software) from another source rather than waiting on iTunes to fetch it from Apple's servers - which tend to get hammered at new release time. So, it kinda becomes whatever people prefer...
So, in a nut shell - it really doesn't matter. Except, we've discovered that a jail broken device behaves better if upgraded after being put into DFU mode, hence the shift/restore process.
Hope that clarifies.
Marilyn