I'm having this same problem. I'm not sure when it started, but by the disparity of documents I had on my iPad (original, stuck on iOS 5.1.1) and my iPhone (4S, 6.0.1), it had to happen in the last month or so. My iPad is not syncing, while my iPhone is doing great.
I found another thread somewhere about MobileMe e-mail accounts being a culprit. At one point, I had two iCloud accounts showing in my Mail, with two different iCloud icons. Not sure when the phantom one disappeared, but this may be coincident with the sync not working on my iPad.
Anyway, I spent a few hours last night with an Apple Genius at a retail store. She was nice and eager to help, but I left with a worse situation than I had arrived with. I had a good backup in iTunes of my iPad, but I found after having the iPad wiped and restored from backup, that the documents that were stored on the iPad and not synced, just disappeared. Any document I created after the syncing broke, was just gone. Also, none of my apps were returned to where they belonged. I wish I had thought to e-mail my iWork documents to myself. Lesson learned.
The wierd thing, is that after installing iOS 5.1.1 freshly, I can download Numbers and sync back and forth to my iPhone. Unfortunately, this doesn't have any of my other data from all of my other apps. If I restore from backup, then syncing stops and at best I have the "need to upload" arrow on new documents, and none of my existing documents.
I'm so frustrated because I was finally gaining trust in iCloud. It just worked, until it didn't.