I'm intrigued by how you plan to use the iPad, Jim. I saw in another post that you were planning to use it 99% of the time as a remote control for your MBP, and that sounded interesting.
Regarding your question here, I understand your feelings. I have an iPod and have used it in disc mode to transfer files. I have also been able to connect BlackBerry and Windows ME phones to my computer and use them in disc mode to transfer files. I was quite surprised that the iPad does not do this.
In order to use the iPad in a sort of disc mode-like operation, you need to get an app that supports it. For example, GoodReader is very useful in this respect. It's only 99 cents in the App Store, and it does all kinds of cool stuff with files. You can transfer files to/from GoodReader through iTunes or connecting directly to your MPB (or other computer) via FTP or wireless.
Based on your questions, GoodReader's not likely to do quite everything you'd like it to do, but it may well give you a leg up toward at least part of your goals.
As for your process flow and backing up, you have the right idea. Your apps will be backed up via the process you described - and for the iPad, Apple has a workflow that enables you to reinstall apps that somehow get lost without you having to pay for them again. But, no, you won't be able to SuperDuper! clone your iPad or access your apps' data directly for the most part without possibly jailbreaking the iPad - which would void your shiny new warranty.
