I really hope that Villeneuve will get the chance to turn all the books into movies. He gets the vibe of Dune, and the last two books would make for some epic films on the big screen. But to get those made, Villeneuve would first have to do the impossible and somehow turn God Emperor into a movie that wouldn't tank the franchise.
I’ll be happy even if he stops at Messiah, because at least he can end Paul’s arc and realize Frank Herbert’s message about the dangers of messianic figures. GEoD is definitely a difficult task to translate to the big screen. I think it would work if they take Children and God Emperor to the small screen as limited series shows.
As far as I recall from some interviews of his from the summer, his inclination is to end the story after making it a trilogy with Dune Messiah. So, practically he is focusing on Paul's story.