which is fine, i think, because the film makers hit all the major points of the Dune Messiah (Muad'dib's blinding, Chani's Death and Leto and Ghanima's birth) into the series. they did mess up on Alya's Age. she should have been much younger in the Messiah Parts (not that i'm complaining, since the Actress was smoking hot), and Leto and Ghani should have been quite young as well. other than that, they did pretty well.
I Love all the Dune Books, but to me it seems that Dune Messiah was a transitory book, shifting the status quo from Dune to the one in Children of Dune and onwards, basically the deconstruction of Muad'dib's Myth.