I see your point, and USB Mass Storage is a good thing, but using your work file example.
So, it is a file that an application on the iPad can read and write and edit yes? I believe that the APIs allow for an attachment like that to open an application. So, you email the spreadsheet to yourself, you pull out your iPad click the attachment and Numbers opens. Much like Cory Doctorow, the iPad is not for you, and much like with the original iPhone, and Windows Phone 7, they are trying to anticipate use cases and create methods to handle them. There was no copy&paste on the first iPhone, but if there was a phone number in an email or on a website, you could click it and the phone app would open.
Do you use iTunes or another library based music player on your computer ZeroCool? If yes, then do you go through and meticulously change all the files and folders? If yes then I think you are in the minority, if no, then how is that any different? Imagine that entire section of the file system is cut off from you you cannot read/write/see that stuff. So what? Imagine the same if you have Picasa but no access to My Pictures, no access to C:\Windows. You are on your browser, you save a picture, it gets automatically added to Picasa (or whatever you use) and when you want to see it, you would be opening that program anyway.
Please illustrate for me a likely drag and drop scenario where using an intermediary program would not be an option.