I think you need to manually back up in iTunes and encrypt the backup to save the Health data. I wish Apple let you export all your data from the iPhone: messages, notes, etc. as well as Health It's ridiculous that you can't export your own content.
It could be because the iPhone 6 is significantly larger. I've met lots of people who usually upgrade regularly but don't like the new design and are waiting it out. I personally wish I could still buy an iPhone 5S 64GB to upgrade from my 5.
You can use multiple accounts on iOS devices so you could still share apps. Wouldn't be quite as easy unless they are all sync'd from the same Mac in which case it really would be simple.
Incidentally as others have pointed out, you can turn off In-app purchasing in settings.