Pyrrhic Victory: Godzilla succeeds in killing Mecha-King Ghidorah for good, but he's trapped under Ghidorah's bulk, exhausted, and can't continue his rampage.

Ghidorah was the most powerful foe Godzilla faced in the 1960s, requiring the efforts of 2-3 monsters to drive off in his first two appearances.

This movie ultimately heavily criticizes Japanese Nationalism, thus Japanese Nationalism was included, and Japanese Nationalism is what is controversial.

The explanation was that there was a huge controversy over the footage of Godzillasaurus killing American GIs during the WWII sequence.