The app switcher suffers more at times, especially when coming out of the messages app into the app switcher, and going to other apps from it. Spotlight is slightly more sluggish/stuttery as well. The phone struggles slightly more all around with responsiveness/load times but it is still pretty usable. The most apparent thing to my eyes is poor performance with the new notification bubbles. Pulling down the Notification Center if you have many notifications is very stuttery, unlocking the phone when you have many notifications is very stuttery, tapping the search bar on the widgets pane of Notification Center or lock screen stutters a bit. Sometimes pulling up CC or tapping apps or folders has more of a delay than it used to. The app opening and closing animations from the homescreen you mentioned are smooth, and are a pleasure actually, compared to iOS 9.
I'd rate iOS 10 as; a bit slower just about everywhere, but still perfectly usable. Especially if you aren't bothered by frame drops and jitteriness. Reduce transparency fixes like all of the frame rate issues as far as I can tell.