Scenes are pretty heavy weight, in that when they are loaded they have to reset a lot of DOM elements, setup timelines, load images (even if the image is cached, it may need to render and send to the graphics card), etc. Crossfading from one group to another on a scene will be more performant. But the tradeoff is definitely in organization and memory usage per scene.
As for loading at a different scene (I assume you mean via URL?) then this is what I was going to reference: