Rick Veitch has talked about Moore's plan for what a third year for Supreme would have been about. On this page, I said:
Rick Veitch and others have talked about Moore's plans for a third year, with the idea of Supreme exploring inside the supremium meteor. One rumor I heard, which Veitch confirmed, suggested that Supreme would have run into other superman figures from comicdom, perhaps like Moore's own version of Marvelman, etc.
A nice anonymous poster mentioned that Moore spoke about is directly himself.
Moore briefly mentioned in an interview in Kimota! The
Miracleman Companion (on page 23), when he was asked if he had any other
ideas for Miracleman after #16. He said:
"I did have a vague idea that at one point, I remember talking to Rick Veitch: "Wouldn't it be cool if we maybe did a run of SUPREME where Supreme decides to journey to the absolute limits of reality?" Not just to the end of the universe but the limits of reality to try and find out about the nature of this strange form of reality that his universe existed with these constant revisions and the existence of Supremacy and things like that. And I got some mad idea--I don't know how I would have tied it in--that wouldn't it be cool if Supreme reached some place at the end of the universe and went into this room and there was Miracleman and maybe Rick Veitch's Maximortal and two or three other kinda clones of existing super-heroes, all trying to find the answer to the same problem, "Where are we? What are we?" That was the last time that I actually thought maybe it would be fun to have Miracleman turn up in a story. But that's never going to happen."
As an added bonus, Kimota featured a Miracleman commission by artist Supreme Chris Sprouse, to help you imagine the crossover idea:
So, no, it's never going to happen, but it is a fun idea. And if there's a message to Supreme, it's that anything that can be imagined exists in Idea Space. So keep imagining!