I generally hate all the Heisei origins of all the old monsters, aside from Godzilla himself. King Ghidorah himself was flawed for a great many reasons. First off, he is the most iconic arch enemy of Godzilla. And yes, while they were rewriting all the monsters, you first had him in the Showa series as a destroyer of worlds. And then you had Godzilla, who was the defender of Earth. While Ghidorah had destroyed many worlds on his path, he just can't get passed Godzilla, and thus he constantly returns. Four times in the Showa series he appeared to try to destroy earth, each time being thwarted by Godzilla. The Godzilla vs Ghidorah/Planet Destroyer vs Earth Defender feud to me, is very similar and just as epic as the concept behind Superman vs. Brainiac.
His Heisei origin, first off was very weak. As was the entire plot and concept behind the movie in general. First off, you had the plot holes and continuity errors. When the dudes from the future warned about Godzilla destroying Japan, the Japanese people were so confused... "would Godzilla really do that?" And thus even more confused when the new Godzilla didn't seem "friendly." I mean, this was a sequel to GvBiollante correct? We have Miki returning from her role in that movie, where she clearly even makes a reference to events in that movie... where Godzilla was NOT a friendly creature. So why are they all of a sudden speaking of Godzilla as if he's once again Japan's #1 Benevolent Mascot?
But anyways, that's a tad off topic. Godzilla and King Ghidorah. Because of the new Ghidorah origin, and the new Godzilla origin for this film, their fight didn't seem to hold any real importance. They were basically two unstoppable destructive forces who just happened to get in each other's way and fight each other. And because of this fact, the viewer really doesn't know who to root for when Godzilla and King Ghidorah actually face off.
It was a nice try I guess...
However, I still think they could have done a much better job with King Ghidorah in the Heisei series, even with that silly origin. First off, he should have appeared in more than just one movie. And Mecha King Ghidorah... eh... perhaps never should have happened, however, it was an interesting idea, I'll give it that. But he DEFINITELY should have returned at some point in the Heisei series. And I feel, that the best film for this to have taken place would have been in Godzilla vs. Space Godzilla.
Imagine this concept if you will... Mecha King Ghidorah, laying at the bottom of the ocean, left for dead, missing one head that was salvaged to make Mecha Godzilla.... slowly over the years, regenerates, as he was not actually dead, just in a state of hybernation on the ocean floor. He finally is whole again, and seeks his revenge on Godzilla. However, he knows from beforehand that he cannot defeat Godzilla alone. Meanwhile, Space Godzilla's origin remains the same, as he is created in space, but has no real direction. King Ghidorah flies out to space as SG's contact from Earth, who in turn, guides SG back to Earth to defeat Godzilla and get his revenge. And then Godzilla and Mogera face both Space Godzilla AND King Ghidorah, or him in his Mecha form, if that's how he remains. It definitely would have given King Ghidorah more purpose in the Heisei series, and while he does not have the same origin as a space monster, still could have taken it back by traveling into space for reach Space Godzilla.
That to me possibly could have made Heisei King Ghidorah the BEST King Ghidorah yet written. His origin is fresh, but shadows of his bitter rivalry with Godzilla and his origins as a space monster would have still been seen.