Are you sure it's not just perceived lag from the new animations? My 1020 and 520 are running better than ever (except the battery is draining faster on my 1020 post-update, while my 520 has better battery life than ever before. Very mysterious, still investigating).
But while the new animations look great, they are a bit slower in some aspects. Not because the animations themselves are causing lag, but simply because they're longer than the animations in WP8, and there are more of them. As such, it gives the /perception/ of being slower.
I personally like it, as the animations were stale in some aspects. They look wonderful. For me, everything feels faster and smoother, it's very beautiful. Runs like a champ!
It'd be nice if under the accessibility menu, they added an option to reduce animations (much akin to what Apple did for iOS 7), to help make things less flashy for those prone to motion sickness or what have you, and also for those who aren't fond of the longer animations.