Godzilla vs Kong's ending sets up the possibility of Godzilla 3 happening down the line, including where the character's story could go next. Bringing Godzilla to Hollywood was a feat in and of itself, especially after the performance and general reception of 1998's Godzilla movie. So considering that Gareth Edwards' 2014 Godzilla and Michael Dougherty's 2019 Godzilla: King of the Monsters were both successful, there's no real reason for the MonsterVerse franchise to end here.
The latter film wrapped up its story by making Godzilla the official King of the Monsters, but Godzilla vs Kong gives him two challengers - one in Kong and another in Mechagodzilla - with the Titan fighting both in order to retain control of his position. Retrospectively, Godzilla's actions in the 2014 movie weren't just about restoring balance either, as Dr. Serizawa had said, but was also about maintaining his dominance as the Alpha Titan. Presumably, his storyline will remain the same going forward, unless Warner Bros. and Legendary Entertainment want to go in a different direction.
The way Godzilla vs Kong ends, Godzilla is still the Alpha Titan, but he also shares that moniker with Kong, who rules over the Hollow Earth. If Godzilla 3 were to happen, the story would pick up as Godzilla is patrolling his territory, just like every Godzilla installment in the MonsterVerse has already. Whether the new monster he fights is another challenger is unclear, but it's safe to assume he won't be going up against Ghidorah anymore; having Ghidorah be the ultimate villain in two consecutive movies is more than enough for the MonsterVerse. So rather than see Mecha-King Ghidorah make a sudden appearance, the most logical option would be for Godzilla to fight Destoroyah.
Although Godzilla vs Kong was a versus and team-up movie for both monsters involved, the movie was more of a Kong sequel. Godzilla was the villain for most of the film, and his story threads would likely continue from King of the Monsters' ending instead of Godzilla vs Kong's, since the only thing left over is him remaining king. In Toho's films, it was revealed that Destoroyah was created as a result of the Oxygen Destroyer mutating crustaceans in the ocean. As viewers may recall, the military used the MonsterVerse's Oxygen Destroyer to attack Godzilla and Ghidorah in King of the Monsters, which left the former Titan on the verge of death.
As the opening credits for Godzilla vs Kong shows, Godzilla is virtually unmatched; he's defeated two MUTOs, Ghidorah, Kong, and Mechagodzilla (who was being controlled by Ghidorah). While he had help taking on a few of those monsters, he's still undefeated overall in the MonsterVerse. Destoroyah is Godzilla's toughest enemy and one of the strongest monsters ever created by Toho; at this point, Destoroyah is the only one who can build upon what's already happened in the MonsterVerse. Godzilla's win against Mechagodzilla and Kong solidifies that.