My comments are based on a fairly extensive knowledge of xenobiology and some strategy.
Ultimately, this is a fight between a giant reptile and a giant primate, and there are relative biological advantages and disadvantages that each would have.
While Kong is clearly a giant primate, Godzilla may or may not be a giant reptile. That question has major bearing on combat. If Godzilla is a reptile, then he is cold-blooded. However, the mutation enabling radioactive breath could also give him heat generation. I stipulate that Godzilla must have both radioactive breath and maple-leaf dorsal spines; without these features, it is a giant lizard but not Godzilla.
A warm-blooded creature moves faster than a cold-blooded creature. If Godzilla is cold-blooded, then Kong has a very large advantage in combat. In snake-vs-mongoose, the mongoose almost always wins.
However, a cold-blooded creature has an advantage in surviving resource-poor environments. If the two were stuck in an isolated area, Kong would starve before Godzilla.
If Godzilla is warm-blooded, this would partially or wholly negate the mammalian speed advantage.
Another consideration is Kong's intelligence. While not quite human, it is clearly well above animal level, meaning that he probably knows his own strengths and weaknesses well enough to make good combat decisions, and quite likely can analyze his opponent's during a battle. Godzilla has a big head, but here his reptilian ancestry is a severe disadvantage; he probably isn't much smarter than an ordinary lizard. That means Kong will gain a strategic advantage that increase over time interacting.
Either way, like us, Kong has thick muscular legs geared toward walking and running, and large free arms with grasping hands, enabling him to use tools.
In a manmade environment, or somewhere like a jungle with lots of things to grab, Kong would have an advantage due to tool use. He can throw things, which gives him a ranged attack.
However, Godzilla has radioactive breath. This ranges in strength from merely singing things to vaporizing buildings, depending on iteration. If at low strength, this is of little use against Kong, who can ignore heavy artillery. If at high strength, however, anything that could vaporize a building should also vaporize Kong, meaning that Godzilla would only need to land one hit to win. Further advantages are that the radioactive breath seems to travel at extreme speed, much faster than a thrown object, and it is a beam that can be swept over a large range. Even though Kong is fast and agile, Godzilla likely has a large edge on ranged combat.
Strong, agile, comfortable on land and with the unparalleled ability to use tools and throw, Kong would be a brutal force in a fight.
Kong clearly fights better on land, while Godzilla fights better in water. With a waterfront battleground, they are equally matched in this regard. If only one environment is available, then one of them has home court advantage.
The easiest way for Godzilla to kill Kong is simply by dragging him underwater and waiting for him to drown. Crocodiles use this method to kill prey much larger than themselves. I further note that Godzilla's powerful tail means that he could probably perform the crocodile's signature death-roll, especially if he closed his jaws over a vulnerable part of Kong such as the throat or belly.
Conversely, a great ape's crushing grip would be greatly limited by Godzilla's defensive spines, unless these could be broken off somehow first. While Kong likely has the strength to strangle Godzilla, it would be difficult if not impossible to get a good grip for doing so.
Godzilla would likely favor his robust tail for both offense and defense – much like modern-day large lizards that use their strong tails as whips. Scale up that strength to Godzilla's size, and that tail becomes a lethal weapon – which he has used before.
True. Godzilla has an extra limb; Kong has thumbs. While either could be the winning factor, they largely balance each other, because each combatant has a unique way to manipulate the environment.
On defense, Godzilla has the edge, with thick scaly skin and sharp spikes. He might even act like a porcupine, turning his back to a rapidly approaching threat. However, Kong's superior agility on land should be able to offer him some protection as well.
Well reasoned. Bear in mind that combat includes both offensive and defensive aspects. To win, you have to drive away, cripple, or kill your opponent. Given Godzilla's strong physical defenses, Kong might have trouble actually disabling him. Conversely, Kong has less ability to avoid damage but (if Godzilla is cold-blooded) better ability to avoid it.
And lest we forget, the tipping point for Godzilla is that he has atomic breath! Until researchers find evidence of a dinosaur or animal with something like that, though, I will have to reserve my scientific judgment.
Not quite, but there are related examples. Plants directly harness the power of the sun via photosynthesis, which is the discovery that flipped Earth from a reducing atmosphere to an oxydizing atmosphere. Various species have chemical defenses, and at least one -- the bombadier beetle -- generates explosions.
Consider also escapes in a losing scenario. Kong can jump; Godzilla can't. In an open terrestrial environment, especially a 3D one, Kong could escape Godzilla. However, Godzilla is largely aquatic and rather iguana-like whereas Kong's ability to swim is limited if any. In an environment with open waterfront, Godzilla could escape Kong.
I find that the most important variables are 1) whether Godzilla is warm-blooded or cold-blooded, and 2) the exact scenario of combat. A warm-blooded Godzilla would probably win; a cold-blooded one is a closer match for Kong. Due to their very different capabilities, however, the terrain and details of engagement give each one a strong advantage in different cases.
You know what would be really awesome? A game allowing for different variables between the characters. So Godzilla could be warm-blooded or cold-blooded, have a weaker or stronger breath weapon, be able to submerge or function on land for different times. Kong would have different levels of strength, speed, dexterity, intelligence, etc. They could fight in a variety of environments such as jungle, tropical island, open water, tundra, desert, and so on. These variables would determine who had an advantage in any given conflict.