I believe you might be viewing these changes as something that improves persistence/loading/saving but that is not exactly the intended effect of this change. If you're wondering how this is useful:

This allows you to build tooling, such as inspectors/editors, that display or otherwise utilise the currently playing animation, including its elapsed time, speed, whether it's repeating, etc.

animation_clip: Handle<AnimationClip> allows such tooling to link to the definition of the animation; in the defining GlTF, for instance.

path_cache: Vec<Vec<Option<Entity>>> is fairly inconsequential/not very useful from the perspective of something like an inspector or editor. It could arguably be #[reflect(ignore)] but it's fairly innocuous and potentially quite useful for a script or debugger to be able to access.

I have mostly used the example use case of editor/inspector here but the same can be said for scripting.