In my opinion? Update all your apps, do a full back-up to iTunes, note the time, then reset your iPad back to factory so it's completely blank. Perform the update and once it's in, restore from that back-up. The two chief issues people seem to be running into are:
1) They get 98% done, the server times out, and iTunes kicks them back to Step 1, doing the full recovery bit again. This is the longest part and since my iPad was empty, this took no time. The install failed on me 5 times yesterday and I was still done in 30 minutes.
2) Your set-up gets hosed for who knows what reason. Files or apps are missing, data is gone, configurations are jacked up. On an empty iPad, you've got nothing to get messed up, The restore puts you right back where you were, except the new iOS is under it now.