I agree. I'd like a little more control over what goes to iCloud. Having said that, the Documents folder is a fairly recent invention by my standards and I still file quite a bit of stuff in the home-grown document filing system established years before. It wouldn't take too much effort to shift most of the Documents folder contents out into the old system, leaving only the more current files which might be useful to share through the cloud.
You haven't seen my Desktop - I say that with some confidence since it isn't in the cloud yet!
My justification for continuing with the current state of semi-organised chaos is that, based on experience in the physical world, after a virtuous spell of tidying up, it is impossible to find anything ever again.
Euan Williams 