Due to Junior's Gentle Giant nature, he's mostly likely the reason why Japan is a Superpower nation. Plus, he would also be like Godzilla of the Showa series when Godzilla of the time becomes a Gentle Giant with good intentions.
In Godzilla Final Wars, Godzilla takes longer to defeat Anguirus, Rodan, and King Caesar. When he's shown curbstomping the vast majority of the other monsters very quickly. Why? Because he's trying to spare them. Body language in the beginning also shows that he's surprised Anguirus is trying to attack him. What other reason would there be for him not one-shotting them like he did everything else?
Godzilla's main rival is King Ghidorah. Ghidorah is a multi-headed and multi-tailed dragon that terrorizes Japan. Godzilla, in the first film, is worshiped on a small island as the "God Of The Sea". Godzilla saves Japan from Ghidorah. Hmm, a multi-head/tailed dragon vs a sea god. It's pretty much a Shout-Out to Susano VS the Yamato No Orochi.
Ironically, the roles are reversed in GMK. It's Ghidorah (who is actually stated to be a juvenile Orochi) who is the good guy and Godzilla who is the villain.
Godzilla (1998) saw a Godzilla that was almost nothing like the original. Godzilla, Mothra, King Ghidorah: Giant Monsters All Out Attack gives a retcon that it was simply mistaken for Godzilla. This...actually makes sense. Recall the 1998 film. The only thing the Japanese fishers saw of "Zilla" was a spiny tail and a familiar roar. And when asked what he saw, the survivor answered "Gojira". Not "a monster", Gojira specifically. That means that, like in all continuities, the original 1954 film (let's say the 1956 US version to be nice to the US) is canon. Thus your clue is right there from the beginning. The monster wasn't Godzilla at all. Disappointing, maybe, but it gave Toho a good escape clause.
Actually, this troper read both the official screenplay and novelezation. Quite a bit was cut for the movie. The screenplay explicitly states that the only part of the 1954 movie that is "canon" to the 1998 film is the legend. In the film, "Gojira" is merely the term for a gigantic, marine dragon from Japanese myth. The cook was referring to Zilla as a MYTHICAL CREATURE, likely one his grandparents told him about.
Still, didn't end up in the film so we are free to assume the above is true.
I've read in Mothra's bio that over the years she gains new abilities and powers. Not exactly exciting, giving that she is just a butterfly that has to go up against a three headed dragon and a lizard that breaths atomic blasts. Then I thought about the fact that Mothra is a Legacy Character. She passes on her legacy through her heirs and offspring. So, why does is this fridge brilliance? Because she is preforming a sort of Evolution, not against the environment, but against her enemies! She's preparing and bettering herself/her kids for the challenges that they'll/she'll face in the future!
The ending of the 1954 film Gojira has one of the main characters pointing out that he doesn't think Godzilla is the only one of his kind. Then the sequel Godzilla Raids Again comes out and it's confirmed that there is indeed another Godzilla. Let's think about that for a moment. There's not one Godzilla, but an entire species of Godzilla. That means that anywhere in the world could be attacked by one and there's virtually nothing that can stop it.
Used in the 1991 film Godzilla vs King Ghidorah. The Futurians went back in time to prevent Godzilla from existing (so they could Take Over the World, of course) by time-teleporting the Godzillasaurus that became Godzilla from nuclear testing. Except they accidentally targeted the second Godzilla (the one that appeared in Godzilla 1985 and Godzilla vs Biollante), which was later mutated into Godzilla anyways, but with modern nuclear technology, resulting in an even larger and stronger Godzilla.
The Oxygen Destroyer. Long story short, it kills its victims by asphyxiation. To make matters worse, end the end, you're either reduced to a skeleton... or dust. It also doesn't help that the Oxygen Destroyer is worse than the atomic bomb and is the only weapon powerful enough to kill Godzilla. Then, later in the Heisei series we find out it spawned something much more evil than Godzilla.
Adding to this, if Godzilla hadn't been inadvertently freed by the Saradian agent in Godzillavs Biollante, indirectly causing most everything post Mothra, Destroyah would've utterly destroyed all life on earth since there wouldn't be powerful enough monsters and tech to stop him.
In the 1964 film, Mothra VS Godzilla, the egg hatches into twin Mothra larvae. Ok, nothing scary about that. But, the next film that came out the same year, Ghidorah: The Three-Headed Monster, there's now only one Mothra larvae. So, what happened to the other one? It's implied in the film that the other Mothra larvae died. And, remember how Godzilla wanted to eat the egg in MVG?. Also its injuries fighting Godzilla may also be a factor as Godzilla smacks the poor thing with his tail.
Godzila Junior. Sure, he starts out cute and cuddly. But, now take into consideration that he's all grown-up and possibly even more powerful than his father.
Also, the fact that Junior's (And Minya's for the Showa/Final Wars era) existence implies that not only is there an entire species of Godzilla, but that there's a breeding population. Considering how destructive one Godzilla can be....
In Destroy All Monsters, The monsters, namely Godzilla knew where the Kilaaks's base was. If you think about this, that means the original Godzilla knows where and what he's targeting.
It's been explicitly stated that Godzilla absolutely hates humanity (with only a few notable exceptions) due to them mutating him into a monster via nuclear radiation. You think a giant monster mindlessly rampaging across a city is bad? Try dealing with a monster that not only knows where he is and what he's doing, but is deliberately trying to wipe out all of humanity as an act of vengence.
King Ghidorah in GMK is said to be an immature 8-headed dragon. Plain ol' ordinary three-headed Ghidorah is one of Big G's greatest and most dangerous foes in any of either monsters' incarnations. Now imagine Ghidorah with eight heads, at full power and mad as hell. He'd be un-freakin'-stoppable.