I've noticed that several iPad owners (who bought their iPads specifically for this purpose) have gone back to using hard copy merely because transferring the PDFs to their iPads was too much of a PITA.
I've never really had a problem with this. If you want to add them from your computer, you'll need to use iTunes (or if you jailbreak some other program to sync them). Otherwise, if you open a PDF file on the web, you can just download it to the device.
The biggest PITA is just having to use iTunes, which has entirely too much other bloat for a syncing program. Really, Apple should separate iTunes into different programs. One is the content store, one is the media player, and the other is the syncing program.
The sync program should also allow a dropbox like feature where you can specify a folder and have any content in it synced to the iDevice, and allow the ability for this to occur wirelessly.