The King Kong in this movie was a force of nature not just a Giant ape.
Unlike the original who was just a species of giant ape (the DVD of the Peter Jackson movie even scientifically catagorizes him as MEGAPITHECUS), in THIS movie he's an island god. An elemental force given flesh and is therefore a match for Godzilla.
This movie was a clash of elemental forces.
Godzilla represented the unlikely but obvious combination of Fire and Water. He rose from the depths and crushed everything in his path like a tsunami and spat searing hot irradiated flame.
Kong represented Earth and Air. He was as strong and as sturdy and unyielding as the mountains he lived on and then drew extra strength from the air above in the form of lightning.
That's why the battle could have gone either way.