There is a lot of space for improvements:
1) When applying animations from the Magic Animator, while it is an amazing feature itself, it should be possible to choose at least the duration of the single animation. Some of the pre-made animations, in fact, last too much for a 15sec Banner. The possibility to specify a custom duration for the Magic Animation you are applying should be considered.
2) In every banner I've designed in my long experience (15 years) there are ALWAYS some elements that live in multiple scenes, image footers or headers containing logos and disclaimers, placed over some shape. It should be possible to have a way to tell the system that some elements should be in the next scenes as well, without manually copying them, because copying things almost always duplicates elements, creating many useless duplicates all along the scenes, and when this duplicates contain texts, you have to manually change each one of them if your text changes later. Moreover, even following all your best practices, like building a fully finalized first Master Banner, does not prevent you from having to manually copy and modify each recurring element (shapes and texts) between scenes FOR EACH SIZE later generated, with a lot of effort and time loss, and DOZENS OF DUPLICATED shapes and texts.
The unique working solution, right now, is to keep your entire banner in one scene, loosing all the advantages of subdividing it in multiple scenes to fully use the transition between scenes.
My suggested solution could be a flag on each layer, similar to the "lock animation" one, to tell the system that the flagged layer should be kept in any scene as it is.