Currently Scene.MouseHandler is called on every pulse, and if there's was a single mouse event, it will continuously go through the list of nodes, doing picking etc, even if the mouse is off the scene.
MouseHandler.process() is the number two allocation spot in the profiler for the new stack (there's more pressing stuff in the marina stack that's even worse).
To reproduce: run attached app with preset number of nodes (like 2000), move the mouse over the scene, notice that MouseHandler.process() is called even when the mouse is moved from the scene:
javafx Fire -2000