I was having the same major issue with Numbers not syncing since upgrading to iCloud Drive. I have probabaly around 50 spreadsheets that I have been using without any major issues for a couple years. I upgraded to Yosemite, but that didn't solve anything. After toggling off iCloud Drive on my iOS devices multiple times, signing out of iCloud on them multiple times, and endlessly restarting my devices. This is what seemed to have solved ot for me. At least so far.
I am running OSX Yosemite on my iMac and iOS8.1 on my iPhone 5S and iPad Air.
I turned off iCloud Drive on my iOS devices.
Logged onto iCloud.com.
I opened every spreadsheet, and noticed that likely 90% or more of them had developed a sync conflict at some point. Not sure how that happened as I hadn't used some of these for many months. Also, the conflict had a spreadsheet from each device with the exact same timestamps. I chose to keep the iCloud version.
I opened each spreadsheet, and made a very slight modification to force it to save a new version.
Once every spreadsheet said that it was last updated "Today", I picked up my iOS devices and turned iCloud Drive back on. They began to download my entire library. This took a little longer than I thought it should have, but I was patient and waited for them to finish. Once they finished, I created a new spreadsheet from each device and named it based on what device i created it on. They all synced properly. Then I tested by opening different ones on different devices, and all the changes seem to be syncing properly now.
Maybe my iCloud Drive was getting hung up on all of the sync conflicts that I was unaware existed.
That's what worked for me this morning. Clearing up all of the sync conflicts.