I can't be positive, but likely an App - and it might not be the ones that you think are to blame. I am constantly changing things around on my iPad (got the 16 Gb, and so am always running out of room), and sometimes backups are fast, and other times slower. But, who has time to see whether each app causes problems or not? There could be memory leaks, etc that would cause an app to cause slowdowns. I only use Pulse, and now the USA today app, but have no problems with that. Sometimes doing as back up / restore will help, but not always if the app is doing funny things, and since the app does not necessarily crash, no one knows (including the dev) that it is causing problems. Also, when I was jailbroken, there was slowdown then as well, but I know others that had no problems with jailbreaking causing slow downs.
If you have only few apps, and some time - you might try doing a new setup and then install one app at a time, and do a sync in between installing new apps (you have to unplug and then re-plug the ipad in). Then when things slow down, you likely have your culprit - yeah , I know - what a PITA!! I would only do this if I only had a few things.. Good luck.