What those guys said. Could not have said it better myself.
I would put in a vote for embedding codec within media file - is that even possible? seems tricky considering there may be revisions and updates to the source?
My request would be for EXR-like multiple layer support, but maybe that's asking too much. But even an extra channel or two for depth passes etc would be amazing. I've always wanted a PSD-like layered video file that didnt have the 32bit requirement overhead of EXR. You could export multiple tracks of animation at once, in a compressed 8bit format, like a layered video .tiff...