As WP 3.5 brings hudge amelioration in galleries and images management, I wonder if File Gallery could offer new solutions. Some suggestions - I understand it's work and you don't need more work :-)
The new media interface is much clearer and easier to manage. It could be interesting to make this interface opening when putting some files on the File Gallery zone.
The new interface shows all the media files in the library: an option to have the same interface only for files attached to the post.
Well, in fact, I would need the File Gallery possibilities in the new interface (choosing directly the featured image, sort order for galleries...). I suppose it's a completely different plugin :-)