Fan-Preferred Couple: The fandom may not be huge compared to other fandoms, but Nick and Elsie is considered to have more chemistry than Nick and Audrey or Mendel and Elsie by several who watch the show.
Ensemble Darkhorse: N.I.G.E.L. Several of the recurring or one-off kaiju are very popular, such as C-Rex, Komodo, and King Cobra.
In Serbia, where Godzilla as a franchise tanks horribly on regular basis, the series was popular enough to become one of only four American cartoons in history to be given a Serbian language dub. Particularly notable was that the entire series was given this, which had only happened once before. Ever.
Harsher in Hindsight: From the episode "Future Shock", "Who's been playing dominoes with the World Trade Center?"
Rescued from the Scrappy Heap: Did this to the original movie... sort of. The movie is still considered not good, but it made the characters from the film, and Zilla, Jr. himself, much improved from the original form, and powerful enough that they could call it Godzilla again.
Nick is much better received as a protagonist in this series than in the movie proper. Helps that he gets actually awesome moments, has character development and isn't just an awkward character that really annoyed people.
The original monster, as was stated previously, was not popular. He gets brought back from the dead as an alien-controlled cyborg monster, in one of the most memorable stories in the series.
The Scrappy: Audrey is just as disliked here as she was in the movie. Probably doesn't help that she doesn't seem to have learned her lesson and to top it off comes across as really clingy and selfish.
Strangled by the Red String: Many fans wonder what Nick even sees in Audrey at all and why he continues to put up with her. The relationship has been criticized to feeling very forced. And while not as criticized as Audrey and Nick, there are several in the fandom who have criticized the Relationship Upgrade for Mendel and Elsie. It has been argued that while not as bad as Audrey and Nick, their relationship is almost just as forced.
Surprisingly Improved Sequel: The animated series fixed a number of the main criticisms leveled against Godzilla's portrayal in the 1998 film, giving him an Atomic Breath, greater durability, and showing him in combat with other monsters.
Ugly Cute: Junior himself, especially as a baby◊ and when he figures out that Nick is "dad" during his juvenile stage. Partly it's the look, partly it's the surprised noise the great lizard makes.
What Do You Mean, It's for Kids?: The series has an incredible amount of violence compared to the film, such as the lead monster dismembering various antagonist kaiju, melting some of them, and even burning one alive. You have to wonder what the FCC thinks about this. It also showed military characters using guns that had the looks of real life guns (despite some Off Model issues) during a time when Family-Friendly Firearms was the norm for most US animation. And in the second episode, Animal flat out calls some soldiers "stormtroopers" to their faces, though the "Stormtroopers" comment might have simply been a Star Wars reference.
The Woobie: Sydney Walker, the man who inadvertently creates the Crackler, in "What Dreams May Come". By the end of the episode you'll wanna give the poor guy a hug.