A/N: after watching Both of D Man1954's videos on about either kaiju on them becoming the villain. However, I decided to do my own thing on this.

And what I mean from this is how they can do the film without any of the two being the "Villain Kaiju".

Now anyone who's watched Kong: Skull Island and read it's sequel comics knows that there no way at Kong being the bad one here.

As Monarch embarks on a perilous mission into uncharted terrain and unearths clues to the Titans' origins, a human conspiracy threatens to wipe the creatures, both good and bad, from the face of the earth forever.

First, let's look at the personalities of the two kaiju.

Godzilla: 

Monarch describes Godzilla's behavior as that of a "protector," calling him an "ancient guardian of the natural world." While Monarch initially considered Godzilla to be a threat, it now considers him the potential greatest defender of the planet, as he emerges to battle any aggressors which threaten the balance of nature. Whenever Godzilla is not enraged and in combat, Monarch describes him as "slow, graceful, inquisitive even." 

Godzilla (2014), Godzilla's behavior seemed to be that of a territorial animal. Ishiro Serizawa theorized Godzilla is the driving force to restore balance to nature whenever that balance is disrupted, suggesting that he essentially considered the entire Earth to be his territory. However, unlike previous incarnations, he doesn't blatantly attack or plow through ships at sea simply because they are there. In fact, with larger ships like aircraft carriers, he simply dives down under them. 

(Though what happened to the U.S.S. Lawton may have been an unintentional act from Godzilla whether or not if he was the one who did it).

Even when he was attacked by the military, he didn't noticeably react or fight back and simply continued to hunt the MUTOs, even when being followed in close proximity by four naval ships. He only reacted by this when they shot him in the gills and he ran through a part of the golden gate bridge, showing it wasn't an intentional act of destruction, rather him just responding to his weak spot being hit.

He showed little interest in humans, instead focusing his attention entirely on the MUTOs. After defeating both MUTOs, he left the humans alone without any more conflict. In Godzilla: Aftershock and Godzilla: King of the Monsters, Godzilla continued to behave in this manner. He maintained a patrol route around his territory, and used his glowing dorsal plates to perform an intimidation display. While Monarch initially assumed Godzilla was demonstrating aggression toward them, they later realized he was reacting to the presence of the ORCA before pursuing it to Antarctica. Godzilla recognized the threat posed by his ancient nemesis, King Ghidorah and goes out of his way to seek out and try to defeat Ghidorah on three occasions. Godzilla recognized Mothra as his ally and communicated with her through sonar. He demonstrated inquisitiveness toward humans, first when he saw Serizawa approaching him and placing his hand on his face, and later after he resurfaced and leaned forward to inspect Mark Russell. Godzilla never demonstrated outright hostility toward humans when he noticed them, and allowed himself to be surrounded by a full military escort when he headed to Boston to confront Ghidorah. As the new alpha of the Titans, Godzilla was said to actively steer other Titans away from human cities and prevent any further destruction.

Kong:

Kong is the guardian of Skull Island, and is responsible for maintaining the natural order and defending the island's wildlife from threats. While Kong appeared to be highly territorial, he did demonstrate some degree of altruism, such as rescuing a trapped Sker Buffalo and saving Mason Weaver from drowning. Kong was not normally aggressive towards humans, and only attacking them when provoked. This was seen when they started bombing the island when arriving. The native Iwi tribe revered Kong and view him as their savior, as he and his family allegedly defended them from the Skullcrawlers in the past. Kong demonstrated an interest in Mason Weaver, as he at one point allowed her to touch her face, and later admired her in his hand after he rescues her from the Skull Devil.

So with this Godzilla, he's more of someone who does what he can to keep balance and order within nature. And it was with creatures like the Mutos, MUTO Prime and King Ghidorah who were one's that would have destroyed that balance. The Mutos and Prime would have massed produced their species and Ghidorah was regarded as a living extinction event and was going to use the titans to fit how he wanted earth. Godzilla reacted to when these creatures attacked to prevented them from doing these acts. It's not just for ancient rivalries, he's trying to prevent earth from being over ran or destroyed. And with humans, he doesn't see them as much of a massive threat since they've yet to do anything to show themselves as a threat. 

However, King of The Monsters may show a change in this as he was hit by a Oxygen Destroyer from them, which resulted in him almost dying. Godzilla may also come to the idea that humanity is likely to make more of that weapon to use against other titans and even kill them. Godzilla would have to take matters into his own hands to stop them from trying to make more of these and try to set an example towards humanity to not disrupt the order. The other idea could have to do with what was seen in the credits of king of the monsters, it was said that Monarch had an outpost on skull island and that in the past, they were attempting to create Organic Titans and are working on a Mechanical Giant.

(A closer look)

So Godzilla may head off to Skull Island and attack the outpost on Monarch to try and destroy said mechanized giant before it can be used. Same with any organic titans they may  try to make, Godzilla may attack to destroy it, leading in humans getting harmed,to which Kong would eventually appear and fight with Godzilla to protect the humans, not properly understanding what it is Godzilla is trying to do.

Godzilla likely won't try to communicate to Kong about the thing because he'll probably see Kong as some sort of enemy Alpha or whatever. Leading to where the two will fight one another, and of course, the military will be involved to try and stop the fighting, or kill godzilla for attacking.

So, this is at least how I think they can do this without having where one of these two titans is a definitive villain that we should just be rutting against in the film.

Plus, the description for the film brings in a little more to what we may be in for.

"In a time when monsters walk the Earth, humanity's fight for its future sets Godzilla and Kong on a collision course that will see the two most powerful forces of nature on the planet collide in a spectacular battle for the ages. As Monarch embarks on a perilous mission into uncharted terrain and unearths clues to the Titans' origins, a human conspiracy threatens to wipe the creatures, both good and bad, from the face of the earth forever."

Notice the last part of that.

"As Monarch embarks on a perilous mission into uncharted terrain and unearths clues to the Titans' origins, a human conspiracy threatens to wipe the creatures, both good and bad, from the face of the earth forever."

Monarch Embarks on a mission in uncharted terrain and unearths' clues to the titans' origins and a human conspiracy that wishes to wipe out all the titans.

So that could hint at much more going on. So, this Conspiracy could also play a part in getting Godzilla and Kong to battle and try and kill each other.

But, those are all the assumptions and stuff I have on how this can go to where neither Godzilla or Kong are painted as either of the ones in the wrong within this film. Both of them have a reason to do what they do, Godzilla maybe trying to do what he does to restore balance and Kong fights Godzilla to defends any humans he may attack.