That actually sounds, like a really good idea. It would seem to give a feeling of sadness and remorse, but changes to anger, because Dedede is facing the one who defeated him.
I myself am a big fan of those themes as well, and I have heard a ton of different musical styles for these themes. I have an idea, when playing the opening part from "Fountain of Dreams", instead of playing a piano, I would love to hear an organ, because it add an atmosphere that would intensify the feeling of remorse, and also add a hint of eerieness.
I agree with you on how the ending should be, fading out instead of just suddenly stopping. I always found that those that suddenly stop a little unnerving, because it yanks you out of the state of relaxation you enter when the song ends.