The fact that SkyDrive doesn't allow syncing of arbitrary folders is super annoying. So I wrote a small ShellExtension that is doing the job. http://janhannemann.wordpress.com/2012/04/26/sync-any-folder-to-skydrive/
Go and get it if you like it.
Heh, funny, I had suggested that approach during dogfood. The "problem" is the sync icons only show when you go to the directory under the skydrive folder.
I'll be sure to forward this thread to the team though.