Hello.
As you may have guessed, this story will never be finished. At least, not in the foreseeable future. I love this concept, and I had so much planned for it, but I no longer have the drive to finish the story at the level of complexity I wanted to.
As an apology/compromise, I am posting the snippets I had written already. I hope you enjoy them!
SPOILERS
Hughes lives. Roy is the one who "dies" because he gets too close to the truth. In actuality, Father uses him to make a new Greed, so we have Greedroy instead of Greedling. That's the biggest divergence from canon. Because of the change in circumstances, they're able to defeat Father without suffering any casualties. "Just this once, everybody lives." Why? Because I'm the author and I say so.
Al and Ed get their bodies back to normal, Roy and Greed take turns being in control, Riza and Roy live happily ever after together and when she dies of old age, Greed finds a way to release Roy's soul so he can join her in the afterlife. And Greed lives on forever as Amestris' guardian angel. The end.