If anything in this movie can be called "brilliant" the closest thing would be what at first seems like one of the biggest plot contrivances of the movie - how did Michael's dad manage to survive falling into the giant fissure in the Earth, as well as having a tree fall on him? It's because the evil monkey can only kill if it can clash its cymbals together. It could use all of the evil magic it wants, call down earthquakes and storms, but because its arms were tied together it wasn't actually capable of causing death no matter how hard it tried.
Just how is Madeline going to explain her husband's sudden disappearance and her new baby? Especially after she spent the whole of her time onscreen reminding everyone within earshot about her infertility? No one would believe the real explanation (magic) so it's more likely everyone's going to assume that she murdered her husband and stole a kid.
Johnathan Cooper is probably going to kill his wife/mother. Even though he was age-regressed back to infancy there's nothing to suggest that he doesn't still have all of his memories and knowledge. So we have a guy who was already a Jerkass, turned into a kid and being raised by a woman he already didn't like, and he knows magic. (Even if he no longer has the book, he should still remember a few spells, especially since he was speaking them into his tape recorder the whole time.) Mike Nelson was right: clearly, Merlin has brought good into the world.
An infant's brain simply isn't large or complex enough to store an adult's knowledge and personality. So it's more like Cooper is dead.