If you're among the numerous people who bought an iPhone 6s Plus in the past three months, you may have found that your iPhone 6s Plus screen keeps flickering while you're converting between different apps, using 3D Touch or attempting to search something with Spotlight.
The explanation for this is that your iPhone 6s Plus is forced to drop frames when it is dealing with graphically intensive computations and has to freeze before it succeeds to pass the bottleneck. According to Apple's design, the iPhone 6s Plus interface is rendered at 1242-x-2208-pixels and then downscaled down to 1080p.
It does so by using hardware that downscales the image that is projected onto your iPhone 6s Plus screen at a system level, integrating it into the inner mechanics of the iPhone 6s Plus.
Theoretically, there should be absolutely no reason the iPhone 6s Plus screen flickers and freezes at times, but the best guess as to why this happens is because of poor software optimization by Apple, despite designing the iPhone 6s Plus to use a hardware based downscaling algorithm.
Thankfully, there is an easy way to fix the iPhone 6s Plus frame drop issues as long as you're willing to make a compromise. By going to Settings -> General -> Accessibility -> Increase Contrast -> Reduce Transparency, and turning Reduce Transparency on, you'll be able to make your iPhone 6s Plus as buttery smooth as a regular iPhone 6s.
The Reduce Transparency option lightens the graphical workload that your iPhone 6s Plus has to deal with by removing some of the transparent aesthetic features Apple has put into iOS 9. Spotlight, for example, has a grey background with Reduce Transparency turned on instead a murky image of your home screen wallpaper.
As long as that isn't a deal breaker, this fix will at least help you keep your sanity until Apple finally gets around to fixing this issue. You may have to wait until the iPhone 7 however. The iPhone 6 Plus had the same problem.
If you're wondering why Apple even bothers to render the iPhone 6s Plus at a higher resolution, it's to help developers. The original iPhone was based on a 163-ppi screen, while newer retina displays, in iPhones such as the iPhone 4 to the iPhone 6s are exactly twice, at 326-ppi. That means developers only had to scale their assets by a factor of two to keep developing.
The iPhone 6 Plus and iPhone 6s Plus however, are rendered at three times 163-ppi, which comes out to 489-ppi. Unfortunately, the iPhone 6 Plus and iPhone 6s Plus only have a pixel density of 401-ppi.