I think Final Crisis would have worked a lot better from a marketing perspective if DC had just made the Superman Beyond issues (at the very least) official issues of Final Crisis. I know the worry is that there is a different artist, but when the artist is of the high quality of Doug Mahnke, I don't think the readers would have had much of a problem, particularly since J.G. Jones needed other artists to help out ANYways (something that I'm sure DC knew was a real possibility).

I think I would have given Morrison more issues to tell his story PERIOD, but at the very least, I'd have put Superman Beyond as an "official" issue of Final Crisis (#4 and 5, I guess).