Despite being popular among young boys, the show couldn't complete its second season run due to the infamous Digi/Poke (Digimon vs. Pokemon) War where both Fox and Warner Bros. were licensing various collection/game type animes, such as Digimon, YugiOh, and others. This show got lost in the scrimmage.
One of the main reasons why the series is so different from the movie it's spun off from, Godzilla (1998), is that almost all of the production crew were big fans of the original Japanese Godzilla films. Since the American movie's exact details were kept secret, down to the capabilities of Godzilla himself, the cartoon staff had no choice but to base their work on the Japanese movies. Thus, Godzilla Jr. is more anthropomorphic, has the iconic atomic breath weapon, stands more upright and does battle with other monsters.