The files are only moved over when you want them. The only potential problem is that they are not really available if you are not connected. They are not pushed to the phone, and in fact I'm not really sure if you could. The files I use it for are mostly word, excel and PDF files.
Also with the iPad you have access to iBooks, kindle store and B&N. Also for technical PDFs with color plates the iPad has an obvious advantage. For magazines zinio on the iPad kicks ass. The kindle also lacks Apple's patented unicorn dust.