Biollante really is the most ambitious, innovative and well-made film of the Heisei Series but King Ghidorah is my favorite Heisei entry. In the July 2006 interview linked above, Omori said that it was his favorite too:
"Mr. Tanaka’s philosophy was that, if you have an hour-and-a-half movie, you should have a big fight between kaiju at least every 30 minutes in the movie, which makes the best kaiju movie. So, in the first 30 minutes, you see the Godzillasaurus taking on the American army, the next 30 minutes is Godzilla vs. King Ghidorah, and in the last 30 minutes you have Godzilla vs. Mecha-King Ghidorah. So it was as perfectly matched to the producer’s philosophy. Don’t forget about the existence of M11."
"It was the 60th anniversary for Toho. At that time, Toho had three main genres of movies: war, science fiction, and kaiju movies. All these different genres were in this movie, so it was a well-balanced movie, I thought. So, for the 60th anniversary, it was a very worthy movie, which is what the producer and everyone thought. So we had a very [good] balance with the movie itself, and [the battle of] Godzilla vs. King Ghidorah, who had been a really strong enemy, is contained in this movie. Thus, it’s my favorite movie."