I may be wrong here
But I'm guessing, if you added and deleted 100's or 1000's of apps and data files onto the iPad over many months, whilst we can't see it, the files must be getting fragmented.
I'd guess, by just deleting everything on your iPad totally, as if you were going to sell it, then resyncing it to your computer, to copy everything back on, a-fresh, it would all be put back on in a continuous non fragmented manner.
I'm only guessing though, and I doubt there is much noticeable difference anyway.