Shortcake is cool. I don't think it should be in core at this point. Also, I'm not sure why they place the shortcode elements under "Add Media" - you should be able to create your own button in TinyMCE that when clicked will open a modal with only your plugin's specific shortcodes to choose from. Again, I really like the concept behind Shortcake... there's just some critical shortcomings yet to be addressed.