The plot, as with most of the movies in the somewhat unofficial Godzilla Millenium series, is discontinuous and ignores all other Godzilla movies in the Millenium series, including the events of Godzilla 2000. Basically, it's a new Godzilla every single movie.
The director for this movie is NOT the same as the one for Godzilla 2000, and that also explains the different feel of this movie. Only the costume and effects remain the same. For your information, the director who worked on Godzilla 2000 also worked on Godzilla vs Destroyah and Godzilla vs Mechagodzilla in the 90's Godzilla series...which were all some of the best Godzilla movies. If you are one of those people, like me, who found those 3 movies great but the ones in-between so-so, and didn't really know why, well now you do.