These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
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.
Protagonist-Centered Morality: Kind of a strange case in the first two episodes, when Nick claims that the military was "Wrong" for trying to kill Godzilla Junior, as "He wasn't hurting anyone." This despite the fact that the previous specimen nearly leveled the city, and the current one is seen shooting atomic fire out of his mouth, even before the military showed up. In fact, Nick was previously advocating the creature's destruction, and was trying to force the military to do that exact thing. He gets a little better.
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.
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.