Heads up when Upgrading to new iPhone through iTunes

I got a little silly last week and bought an iPhone 6 as well as an iPad Air 2.
I Synched my both through iTunes, expecting a complete transfer to the new devices. That was naive.

Some apps were deleted. In the case of the the iPad Air 2 it was half a dozen. I had to go to the app store and download them all again. No charge, but why?

More irritating is that none of my settings were transferred. I have had to re-enter my logins for everything. DropBox, Evernote, Waze, just to name a few. This is annoying at best. On occasion when I needed information quickly it really pissed me off.

Some of the books I had in iBooks are no longer available.

All my music files are now in the Cloud, and I have to manually download them. I expected them to be transferred directly to my new device.

By the way, downloading music is quirky, to say the least. I think Apple assumes I am always going to have access to WiFi, but I live in a rural area and often cannot access music that's in the cloud. Sometimes, when I click on a "song" (I find it tacky that Apple insists that a Rondo from a Quartet is a "song"), it downloads, but often it does not. The little circle appears but nothing happens.

Silly stuff, like the locations I had in various weather apps were lost.

Overall the experience was frustrating and stupid. Nothing at all like Migration Assistant.

Thank you for taking the time to elucidate the process. I hope your advice helps others avoid the problems I am still dealing with.

My point is that the process of transferring files from my old iPhone to my new one should not be so complex and should not require so many steps. There was a time when Apple's core values were ease of use, awesome power, security and simplicity of use.

At least for transferring files to an upgraded device your solution is not simple, and Apple's instructions on their web site are flat out wrong. Had I known how much time I would have to waste I would not have upgraded.