Yeah, I have always installed as new since my first iPhone 3G. I would have done it this time as well but Apple Watch prevented me from doing that. I started with a backup from iCloud and that was taking WAY too long so I tried from iTunes and that wasn't any better. I had made a backup of my 6 on iTunes that morning just in case iCloud was overworked. Evidently all of the apps in iTunes were way outdated so it was actually the next morning before I had everything from my 6 loaded on my 6s since it had to pull all the new updated apps in.
I sure hope Apple gets the activity and health data separated so you can just pull that in from iCloud next year instead of having to restore an old backup onto a new iPhone.