All I can say is, GMK is the absolute best of the Millennium films (followed by Tokyo SOS). And it's one of the best films, if not the best Godzilla film.
Mind you, there are still limitations to this film: The usage of King Ghidorah and Mothra (at Toho's request) as opposed to Anguirus and Varan (per Kaneko's original story treatment), and the shorter production schedule. Aside from all that, the story was very strong (Kaneko had thought of this story years before it was made!), and has perhaps one of the best presentations of Godzilla in the Heisei era! I will say that this is perhaps the strongest Godzilla film made after the Showa Series. The VS Series didn't come close (despite G84 being the most "down-to-earth" of the films and having the best SPFX of the bunch, IMHO).
"The monster a child knows best and is most concerned with [is] the monster he feels or fears himself to be." -Bruno Bettelheim