Syncing safari bookmarks between Mac and iOS through iCloud messes everything up

I'm not sure if this is a new "feature" with the new Yosemite and iCloud feature upgrades, but I'm facing a severe problem syncing bookmarks between the Mac and iOS.

There's a mac running Yosemite, and a couple of iOS devices on iOS 8. I enabled iCloud and let it sync bookmarks. It's managed to make a proper mess of both my Mac and iOS bookmarks, now, with multiple copies of identical folders and individual bookmarks. What's worse is that it's taken all my nested bookmark folders and tossed them into the top level, while at the same time keeping a copy of the nested folders in my Mac safari bookmarks.

Fortunately, I always keep a backup, so I cleaned out everything on my mac and iOS devices and restored from the old bookmarks after disabling iCloud sync. When I enabled iCloud sync again, the bookmarks on the iOS devices started getting messed up again with sub-folders being migrated to the top level, and this mess was reflected back in the Mac Safari bookmarks.

As a result, I've completely disabled iCloud sync and have given up trying to sync Mac and iOS bookmarks.

Does anyone have the same problem, and if so, did you find a way to resolve this?

[rant] I can't believe they force you to merge all your bookmarks instead of giving you a simple option to replace existing icloud bookmarks with the ones from your browser or vice versa on the iPad[/rant]