No, you're wrong. (Unfortunately.) There doesn't "got to be a simple tool for this" because it runs counter to the philosophy of iOS. However, I suspect you can accomplish your objective with Goodreader.
Okay, that was a rhetorical question...
But now you have my interest piqued... what is the philosophy of iOS? And how does it run counter to it?
I am genuinely interested. I guess I was under the mistaken impression that the philosophy of iOS was to fulfill the needs of its users.
I will checkout Goodreader in the meanwhile. Thanks for the tip.
A couple of tenets of the Apple "philosophy" (at least as far as iOS is concerned) are relevant here. First, you'll notice that there is no common file system on the iPad. That's because Apple believes the data associated with an application "belongs" to that application and should not be readily available to other applications.
There's some justification for this approach, though I find it cumbersome and problematic. The usual rationale for the approach is that such a design goes a long way toward eliminating malware, viruses, etc. from finding their way into the device's OS since the data are segregated into "walled gardens" associated with specific applications.
The other aspect of the Apple "philosophy" is more pragmatic. Avoid if at all possible making it simple to interface Apple products with other manufacturers' applications and hardware unless said third parties are willing to pony up sufficient incentives to Apple and abide by its rules. It's a "philosophy" that is hardly unique to Apple, of course. IBM lived by the same philosophy in 1970.
P.S. Just to reinforce the "Goodreader" option, I think you'll find it an indispensable application for a variety of purposes. You'll note, however, that when you import documents using it that you're putting them under the control (and using the space) associated with that application. Fortunately, Goodreader supports the concept of folders which should allow you to preserve a reasonable level of organization for your documents.
P.P.S. I'd also agree with the poster above with regard to DropBox. I'm not sure if your expressed distrust has to do with security or reliability. If it's the latter, I'd recommend that you never put anything into the cloud that you don't have backed up elsewhere. If you're concerned about security, I suspect that you won't be persuaded by anything anyone could say. In that case, the Goodreader option with a USB cable (or if you're adventurous a wifi connection on your network) may be a better solution.