first of all, I thought that Genpatsu-kun is better than Nuclear Boy because Nuclear Boy seemed harder for little kids to get the idea of nuclear weapons (not that using the word "unchi" makes it easier lol)
like some people mentioned, I thought that the way the narrator spoke was a big difference. The Japanese version spoke like a child's father, while the narration for Nuclear Boy was more like a news reporter.
also, the animation for Genpatsu-kun was more charming.