There is no other way to upgrade/restore/update the iPad's iOS other than to use iTunes. Yes, you can now install incremental updates from Apple over-the-air, but that's the only "different" way, there is no other offline method.
And, I guess I don't understand your question. Unless you are talking about specific jail break tweaks, you don't lose apps and data on an upgrade as long ad you (1) make a backup before the update and (2) restore from that backup once you are on the new firmware. I've been upgrading since iOS 3.x and, using my backups every time, I've never lost data or apps. apple has designed a pretty good system for keep ]ing your "stuff' when you upgrade the iOS.
Now, no, you won't have your jail break tweaks. And, no iOS 6.1.3 is unjailbreakble at this time (and probably never will). But, should we get a new iOS version that is jail breakable, then you'll be able to put your Cydia tweaks back on. Cydia is like the AppStore in that aspect q once you buy a tweak, it's yours and it can be re-installed.
How some of this clarifies.
Marilyn