I haven't noticed any changes in 9.3 animation performance to be honest (iPhone 6). I am overall pleased with the responsiveness already since 9.1, although the animation is still jittery in Spotlight when you use it for the first time after a while.
Based on some experience with other systems, I think that many of these animation issues are related to Apple's aggressive stance on memory and energy consumption. iOS uses a lot of tricks to defer loading of visual components as much as possible and I think the result of this is choppiness in some areas, because they fail to come up with a visually appealing solution. Maybe the issues are in iOS 9 precisely because they introduced new measures to reduce energy consumption, something which they also said they had done (remember the additional hour of battery life?). Otherwise I have no explanation why the Spotlight animation is choppy only the first time and not in subsequent uses; it is likely a (graphical) memory issue.
Based on some experience with other systems, I think that many of these animation issues are related to Apple's aggressive stance on memory and energy consumption. iOS uses a lot of tricks to defer loading of visual components as much as possible and I think the result of this is choppiness in some areas, because they fail to come up with a visually appealing solution. Maybe the issues are in iOS 9 precisely because they introduced new measures to reduce energy consumption, something which they also said they had done (remember the additional hour of battery life?). Otherwise I have no explanation why the Spotlight animation is choppy only the first time and not in subsequent uses; it is likely a (graphical) memory issue.