How to transfer EVERYTHING from my iPhone to iTunes?

Basically I've just purchased an iPhone 5. Last July I replaced my iPhone 4 with another one as I broke it, and ever since (stupidly) I hadn't been connecting my iPhone to my computers for back-ups etc, although I have had iCloud activated and running the entire time (to my knowledge).
Now I've just restored my iPhone 5 from a back-up of my iPhone 4 I've just done (a back-up from the computer), yet the only thing that was restored really and transferred onto my new phone was Spotify and my background. What went wrong? I'll admit since I don't use iTunes anymore as I've moved straight to Spotify, I have little idea how to navigate through the latest iTunes, so there could've been a fault on my end, but I don't know.
TL;DR.. How do I get EVERYTHING from my old iPhone 4 to my new iPhone 5? Not just purchased apps, everything. For example, Whatsapp and all the messages/photo's/video's that have been sent within it.
Thanks for the help in advance!

How to back up
support.apple.com/kb/ht1766
How to transfer apps
support.apple.com/kb/ht1848
welcome

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