This one would be best as an independent, non-mainstream film, but I think it would be interesting:
King Kong Vs. Gojira: Battle of the South Seas
The story is actually set in the South Pacific around the year 1938. It is five years after King Kong was kidnapped, taken to NYC, and ultimately killed after falling from the Empire State Building. Ann Darrow finds herself haunted and guilt stricken over what happened to Kong, and when she hears that Kong may in fact have offspring on Skull Island, she puts a plan into motion to have the giant ape moved from Skull island to a more remote location to avoid exploitation. She is accompanied by her husband, John "Jack" Driscoll, and a young Japanese palentologist named Kyohei Yamane.
The island she selects is Lagos Island, but the island is very strange. The plant life seems very foreign to her, and Yamane states that many of the plant forms were thought to have been extinct since the triassic period. It isn't long before the young Kong runs into another prehistoric beast, an ankylosaurus. Yamane is fascinated but cautious, advising the party to leave the island as soon as possible. Ann refuses to leave the Junior Kong without making sure he will survive on this island, and considers another relocation.
Meanwhile, Carl Denham has also caught wind of the existence of the younger Kong, and is desperate to recoup the massive losses of the destruction and bad publicity caused by the elder beast. He plans on capturing the son of Kong, and making more secure preparations to prevent another rampage through a major city.
When he finds that Ann and Jack have already transplanted Kong Junior, he becomes deranged, believing that the pair had it in for him from the beginning, and decides to get back at them. When Ann convinces Driscoll and Yamane to try to transplant Kong a second time, they find their ship has been sabotaged. Denham radios them, telling them to let him have Kong, or else he will leave them to the mercy of this primitive island.
Kong then makes first contact with the huge Gojirasaurus living on the island. Their first battle ends in a draw; The pre-mutation Godzilla has a broken leg, and Kong is ill from the venomous spray the Gojirasaurus had sprayed in his face during the struggle.
Taking advantage of Kong's weakened state, and figuring he could nab two attractions for the price of one, Denham captures the beast and follows the injured Gojira north to Ohto Island, where the creature already has a reputation among the islanders. After repairing their ship, Driscoll, Darrow and Yamane make chase.
Recovered, Kong and Gojira face off during a powerful storm, laying waste to the fishing village, and battle on into the night. Denham and Driscoll face off violently. As Ann tries desperately to stop the fight between the leviathans, the giant reptile spots her and moves in for the kill. Kong sacrifices himself to save her, tackling Gojira and forcing him off a cliff into the ocean.
This premise takes several instances into play. First off, it helps to explain Godzilla's post-mutation flame breath by indicating that it is an extension of the venom spray the original lizard was capable of. The ankylosaurus is also obviously a pre-mutation version of Anguirus. The design of the Gojirasaurus would basically be the same as the future Godzilla, but with slightly smaller back plates and more saurian skin texture and color, supporting design claims that his grey, lumpy flesh of later appearances is in fact part of the radioactive mutation.
I did take some liberties here by including Yamane in the premise, but it would also help to explain his unusually full knowledge about Godzilla during his 1954 appearance, however, having a paleontologist in the mix would be helpful in exposition. It doesn't necessarily have to be Yamane.
Finally, it makes more sense to have Kong fight Godzilla at a point before the Bikini Atoll tests. Kong has always been portrayed as being between 35 to 50 feet tall, whereas Godzilla was always shown as being at least 150 feet tall. The Godzillasaurus design in the Heisei version of Godzilla Vs King Ghidorah shows him closer to Kong's size.
Bombs versus bombs, missiles versus missiles, and now a new superweapon to throw upon us all! As a scientist - no, as a human being - I can't allow that to happen!