I just thought of another solution:
1. Install “Supersized” as a normal JavaScript Slideshow and call it from your WP header.
2. Write a function to make “Supersized” generate dynamic slides and not use statically coded/listed ones.
3. Make the Slideshow use your WP picture-upload-folder as a the location to pull the slideshow images.
This way you could just tie the JavaScript to your desktop theme and fully ignore it in your mobile one. You could deinstall the whole “WP Supersized” plugin.
This solution though lacks the ability to administrate the slideshow from within WordPress.
Has anyone pulled this trick yet?
Thanks, Arne