So I was able to do this on my iPod 5, iPhone 5S, and iPhone 6 but now that I have my iPhone 6S, I try to restore my older backup onto my iPhone and gets it all down including photos, documents, etc. But it won't transfer my apps anymore. It sorts them all on my phone in the folders they were before but, then start downloading all of them with wi-fi which is using up my internet speed like crazy. Before it would take the apps from iTunes and transfer them through USB really fast. I'm connected and all my apps are on iTunes.
Basically its should be transferring my apps from iTunes, but instead it's redownloading them using Wi-Fi.
I'm not using iCloud.