My 6+ stutters sometimes as well. It's not bad enough to be annoying, but I definitely notice it coming from a 5s where everything was butter smooth.
Yesterday, I also went and checked out many of the 6+s in the Apple Store yesterday, and every one of them had some combination of the same issues I have.
Places where my 6+ commonly lags:
- Pulling down into Spotlight in portrait, then rotating into landscape causes some sluggish animation
- Scrolling down the pictures of "Stills" wallpapers in Settings causes some stuttering. (Though, this happens with the regular 6 as well)
- When selecting a new still wallpaper, it takes as much as 4 seconds to set the wallpaper (you get the spinning icon and "Setting Wallpaper" popup for 4 seconds, whereas on the 6 and 5s, it only takes a second). The only other time I've seen this long of a lag in setting up the wallpaper was with my iPad 3.
- Showing all tabs in Safari in portrait view usually-- but not always-- drops a few frames.
- When tapping on a bookmark from the Favorites list, Safari sometimes-- but not always-- lags for a second before loading the page. On the 6 and 5s, it was always instantaneous.
- There's often some stuttering when you unlock your phone using Touch ID and it lands you on Safari, but the animation is usually smooth if you're landing back on the home screen.
I set up my 6+ using a Restore from iTunes backup, so I'm gonna try wiping and setting up my 6+ as new to see if it helps. But because I was able to replicate a lot of these lags on the 6+s at the Apple Store, I'm guessing it's not my phone or my backup necessarily. Hoping it's just some software issues that will be fixed in a future update.