Good essay! I like how you emphasized the mystical aspects of the film, as Shusuke Kaneko had a great deal of success marrying the kaiju and fantasy genres with his Gamera films. After all, Godzilla is really as much a dragon as he is a dinosaur.
Beyond that though, the mystical aspects of the film work well with the movie's theme of generational gaps and Japan's place in the modern world. Yuri Tachibana is essentially drifting through life, caught up in a crass profession that respects none of Japan's traditional values, a fact which saddens her father, Commander Taizô Tachibana. However, while the film may at first seem condemning of modern Japan, Godzilla's appearance reawakens the sins and the guilt of Imperial Japan and the second World War, and makes the Commander realize that perhaps both generations are at fault. The only way to defeat Godzilla, an evil spirit from the past, is by father and daughter working together. It's a very compelling theme and, honestly, I would be interested in watching the film even if it didn't have kaiju.
I think Kaneko should have been granted his original wish to use Anguirus and Varan instead of Mothra and Ghidorah, as a trio of Baragon, Anguirus and Varan would have worked well as a set of guardian entities due to their similarities to one another and Godzilla; it would have been clear that Godzilla was a spirit like those three monsters that had grown very powerful and been consumed by anger. By contrast, Mothra and Ghidorah both seem out of place and are distracting given how ingrained their identities are with fans. Amusingly, Fuyuki Shinada, the designer of the monster suits for the film, was disappointed that Varan (his all-time favorite monster) wasn't going to be in the film, so he compromised by putting Varan's facial features on Ghidorah's three heads. I always thought those heads looked familiar!
I have mixed feelings about Godzilla himself, as many fans do. Back in 2001, Shusuke Kaneko stated his thoughts on the differences between Gamera and Godzilla:
There are big differences between Godzilla and Gamera, as I'm sure any fan of the genre can attest. In my mind, Gamera is a bit masochistic and Godzilla sadistic. The Gamera formula is that Gamera fights, gets defeated in the middle, then returns at the end and is triumphant. Godzilla is different. From the beginning Godzilla attacks--and he keeps on attacking to the end! Godzilla is not a protector; he is the enemy of Japan.
As with many fans, I do have a problem with this; while Godzilla has not always been a protector of Japan and has frequently demonstrated anger for humanity, outside of this film I cannot recall Godzilla acting in a sadistic fashion. In GMK, Godzilla seemingly goes out of his way to cause death and destruction, even taking care not to miss killing humans when possible (remember the hospital scene?) Even in the original film Godzilla was more a force of nature and a testament to man's folly than he was an avenging spirit of malice, and since that time Godzilla has evolved into a truly ambiguous character. In my mind, that ambiguity is what makes Godzilla such an interesting monster, and when you take that away and make him pure evil he seems like somebody Ultraman should be beating up.
But, my criticisms on Kaneko's approach aside, it is apparent that he thought for a very long time about his vision of Godzilla and took great care to make the film a thought provoking and thematically homogeneous experience. GMK isn't just another popcorn flick; it's obvious a lot of thought and soul went into its creation, and that combined with its impressive execution makes it one of the very best entries in the series, in my opinion.