I wonder about this mystery from time to time as well. I am convinced that while some of that "Other" might be valid data for my currently installed apps, there is some (or a lot of) junk in there as well.
For example, a while back I installed a game that I hadn't played in a while. The game did not use iCloud saves. When I started the game up for the first time, it had all my progress and levels unlocked from the first time I had the game installed months ago. The only thing I can think of is that this particular game stored its save data in the "Other" region and when I deleted the game it deletes the app itself but not the "Other" data that the app has written.
I've done a backup and a restore before, that doesn't help because "Other" is part of the backup.
The only way I know to fix it is to completely wipe the iPad and resync your apps and data back on fresh...but of course you can lose a lot of saved games, etc by doing this.
Overall, I just deal with it...but I strongly suspect that there is some bad file management by iOS and developers behind the scenes here.