First I want to point out something about Dune part 2. Thematically its an adaptation of dune messiah. Obviously the plot is just half of dune 1 but if you think about its function in the context of the movie trilogy it asks the audience to take a step back and consider the consequences and human cost of Paul's actions. Its still sympathetic to Paul because we know he ultimately chose the best future he could from the options he saw but if you look at everything from an outside perspective he's far worse than Hitler.
Now that we know for a fact that Chani doesn't go back to Paul after part 2 we know she had to be pregnant at the end of it or else there simply wouldn't be an opportunity in the timeline for the twins to be born meaning the teenage actors are playing them in the present day of the story. This means part 3 is going to be an adaptation of children with messiah's plot.
I think this is a great call. The main political plot line of children has never been all that interesting compared to the Leto plot line so as long as the substance of the Leto scenes remains intact this could work very well. Furthermore if the plot of part 3 was really just all about how bad Paul was after part 2 it would simply feel redundant, but now that Leto II is in the picture we have the opportunity for a more meaningful critique of Paul for being limited by his shortsighted prescience and therefore not seeing the golden path.
The one issue i see with this is Stilgar though because in messiah he was full fanatic mode and in children he was so much more interesting with his scenes being some of my favorite in the whole book, but if Paul's alive in part 3 he'll need to be more like how he was in messiah.
This does make me wonder at what potential future dune might have as a movie franchise. Before now I always thought that part 3 was the end because it was the end of Paul's story but now that we know it will almost certainly end with Leto II in power its basically removed the possibility of adapting children. A day ago I would have said give the Leto II books to a new director and make them a trilogy then give the post Leto II books to a 3rd director and make them a trilogy. Now it looks like thats impossible to the great dismay of all who viewed Dune as a trilogy of duologies (me) and I wonder where we go from here. A stand alone God emperor movie? A trilogy set during his reign ending with a god emperor movie at the end? A trilogy covering each of the remaining 3 books? I really dont know.