I got my 64GB 6S+ a week ago. I didn't bother restoring from my old 5S backup and instead set it up as a new phone.
After reading this thread, I just noticed it says Used:16.2GB/Available:39GB
Strangely all the apps and data only add up to 6GB.
Can anyone confirm, a restore from backup doesn't fix this?
It'll be a pain to re-download and sign in to everything.
EDIT:
So, I ended up using 'PhoneView' to figure out what was eating up the data. Now, since the day of purchase I had ignored updating the iMovie app (616Mb). Under disks>Downloads, I found a huge bunch of folders taking up about 7GB in space. Each folders payload pointed to the iMovie app. Seems like it kept trying to re-download parts of the update. There were a few other partial apps as well. I deleted all of them and got back 7GB. Now it reads Used:9GB/Available:46GB.
iTunes shows 730Mb in the Others folder. Previously it was 7GB.
Hope this helps someone.