This is something I think has been going on for a bit too long now, so let's get done with this.
So, the two villains mostly being debated about this position are King Ghidorah and Alan Jonah. Let's start with Ghidorah. He's the most active threat of the film, and a genuine challenge for Godzilla. His ultimate goals are terraforming the Earth so that it can adapt to his own biology and thus he can live easier, and this requires that he destroys lots, which in the process would cause mass death at a global level, so it's a purely egotistical goal.
Let's talk about Alan. He appears at the beginning of the movie kidnapping a woman and her child named Emma Russell and Madison Russel respectivelty. It later turns out that Emma is a terrorist herself for Alan's terrorist organization, and she's just as involved in the terror as Alan. Alan is the one who rescues Ghidorah at the beginning from the ice block he's frozen into, so technically Alan is behind everything that Ghidorah does. He's also behind freeing Rodan from his volcano, and when you think about it he's behind Emma as well as he is her leader after all. So, what's Alan's goal? Well, the reason he rescued Ghidorah in the first place was that he knew that Ghidorah would destroy and massacre everything in his path, because Alan's goal is to let the monsters overthrow humanity as he believes that they would take better care of the Earth than the humans. So his goal is genocide on his own race, to simplify it. The biggest problem with Alan being the main antagonist is that he doesn't appear as much as Ghidorah, so therefore I've thought about this...
How about King Ghidorah and Alan just being a Big Bad Ensemble? As in, they share the positias the main antagonists? When you think about it, they're just as responsible for what happens in the movue. Ghidorah may be the most active threat, but when comparing his goal to Jonah's, his goal isn't specified to be genocide, just massacring as much as possible ubtilEarth start's adapting to his biology. That's horrible and all, but Jonah's goal is literally self-genocide. But at the same time, Jonah barely does anything in the entire movie, he shows up to free Ghidorah and kidnap Emma, and then he doesn't do much more, but still, without him what Ghidorah does wouldn't be possible.
And now the third option that I haven't seen been discussed as much, a Big Bad Ensemble between Emma, Alan, and Ghidorah. Emma is more ruthless in her goals than Alan, who is calmer, but even if Alan's her leader, she's just as involved as him. Not only that, but Emma has more screentime than Jonah.
Discuss in the comments.
Oh, and here's a poll: villains.fandom.com/f/p/3179493162221868001