The reason doesn't matter and is not worth discussing, imo.
We know for a fact that the iPhone 6 and 5s perform worse with iOS 9.1 than 8.4.1. If this is deliberate, that is worrisome. If it's not deliberate, it means Apple is somehow incapable of improving or maintaining performance of older devices, which is worrisome as well. Either way, it's bad.
Same feelings here, I expected iOS 9.1 to either maintain or improve on the speed of iOS 8.4.1. But it turns out that's not the case. All of my devices updated to iOS 9.1 are obviously slower than before. It's strange how the world's most valuable company can't assure their software quality matches their top notch hardware industrial design.