Setting up new iPhone 6 issues and major headaches
iCloud syncing over iPhones of different generations can be tricky. I highly recommend backing up your iPhone 5 directly to your computer (not iCloud) and then syncing that back up file to your new iPhone 6.

Once all the old data is on your iPhone 6 you can then sync it to iCloud through your iPhone 6 (which can be done in the background).

Hope this helps.