Follow the link (or just google the phrase, which will take you to the same place):
About backups in iCloud and iTunes.
I did and can't see any significant difference between what's in the 2 backups, hence my request for specific details of what you say is missing. Removing duplicates between the two I end up with this list
- Data that's already stored in the cloud, like contacts, calendars, notes,
- Data stored in other cloud services, like Gmail and Exchange mail
Seeing as how that data is easily re-downloaded during the restore, I don't see a significant difference between an iCloud Backup and an iTunes one (certainly not enough of a difference to worry about it!)
The wording on the two lists is a bit different and they're in a different order, but I think I've done it right: here's how I did it with the iCloud backup item first and the iTunes relevant item second)
Data that's already stored in the cloud, like contacts, calendars, notes, My Photo Stream, and iCloud Photo Library (Photos already stored in the cloud, like My Photo Stream, and iCloud Photo Library)
Data stored in other cloud services, like Gmail and Exchange mail ()
Apple Pay information and settings (Apple Pay information and settings)
Touch ID settings (Touch ID settings)
Content you didn't get directly from iTunes, App, or iBooks Stores, like imported MP3s, videos, or CDs (Content synced from iTunes, like imported MP3s or CDs, videos, books, and photos)
iTunes in the Cloud and App Store content (Content from the iTunes and App Stores)