@eltator - yes I can see how that would be an issue particularly for PDFs in terms of internal metadata support. And as PDFs are the most likely reason to be reading books on an iPad we can't give our usual "PDF sucks, use something else" response
I don't (yet) have an iPad, but can you not share a folder wirelessly from it with your PC? Then just use the normal "Save to Disk" functionality in Calibre? I know there is DropBox available for the iPad so you could definitely do it that way. That would preserve the filenames etc.