I did all my transferring via wireless http/ftp remote access. Or I downloaded directly what I needed from online (like power points). If there was something I wanted on my iPad, I just connected to the IP from my main PC and directly transferred it. pretty seamless and simple.
Or I would upload to dropbox.
I'm not saying it's without limits, just telling how I used it.
If you're going to have a locked PC only accessible via USB then either you need to invest in an AirStash drive (a USB flashdrive that creates it's own network, accessible to transfer files wirelessly to the iPad), or Android tab/phone. However, you're still stuck with not being able to access those PC/Mac files...
If accessing/editing PC/Mac programs is your goal, then clearly the laptop wins. But that's a different argument..
Unfortunately none of this addresses what I wrote before.
The PC is locked down so I can't use wifi/Airstash.
USB stick or USB cable is the only way to go.
IP restrictions doesn't allow to upload to a cloud service (encrypted or not).
Emailing the files to myself is not allowed and the files are too many and too large.
Anyway, the main point I was trying to answer was that an open filesystem that allows hierarchical organizations of files and free access of programs to the files is far superior compared to the locked down app centric way that apple is using in iOS.