An aside, my 8yo son used Porco Rosso as the subject of a school speech about a favourite film. I was surprised how few of the themes were lost on him, especially those of war, comradeship, and the other side of every coin. Not to mention those points that only a child discovering the world can savour, that I'd missed myself (or at least misplaced since I first saw the film at around his age in the 90s).
When I was growing up, for whatever reason, Leprosy was used as the outstanding example of a decease that completely incapacitated and made people social outcasts to the point they were sent off to islands to live with other Lepers. I don't know why this was culturally a big deal, I imagine it to be the same as quick sand for American children, just something adults were panicking way too much about. I am Mediterranean for context.
When I watched Mononoke, the scenes in the Iron Village completely befuddled me for a long time at first. This city both constantly establishes itself as a place with a deeply negative effect on the surrounding wilds. They're actively destroying the outskirts of the forest where a bunch of animal gods live, and yet at the same time, they're all nice, and oddly gender affirming and... The villain employs Lepers.
As in, they had nowhere else to go, so she took them in. And she has no problem taking a gun they built directly off their hands, completely unafraid. I grew learning that Lepers were being thrown out because everyone was afraid and they were highly contagious and no one knew what else to do, so having the villain, unironically, show the grace I learned belonged to "The modern world", was like a brick tossed directly inside my brain. She was the reason Ashitaka was dying, she was the reason the pig monster showed up. And yet, she was not a bad person.
Good art. Felt a lot of empathy for Ashitaka. Thought about it a lot, made me grow a lot. And all because someone in Japan, somehow, laser targeted me on my sensibilities on Leprosy. So random.
I wouldn’t call Lady Eboshi a villain or really anyone in the movie, not even Jigo (no allegiances, just working a job). Everyone has different motivations and the movie is about those motivations conflicting. Not because anyone is particularly wrong or bad, they just want different things. No one is perfect, sometimes pursuing the things we want is destructive to the things others want. The gods tasked with protecting the forest ultimately lead to the deer god’s death.
That’s the joy in most Miyazaki movies. Any other movie would have an obvious evil villain. Miyazaki gives all of his characters motivation that is immediately relatable. Sometimes characters that appear to be villains at the beginning are heroes at the end.
All of these things mirror the real world. Rarely is someone actually intentionally evil. They may have different priorities, goals, fears, and motivations, and those may produce behaviors or beliefs that seem bad, but without understanding the why or what, it’s easy to just assume their “bad” people. Ashitaka doesn’t take the bait and is kind, respectful, and generous to everyone who isn’t obviously doing something atrocious (like the samurai slaughtering peasants).
Princess Mononoke is easily one of my favorite movies of all time and my favorite Miyazaki movie.
I think you're conflating villainy with evil. Eboshi abandons her village for cash in the climax of the film. SHe's told the village is in trouble and says "let them deal with it, mama's gotta make that cheddar"
Jigo lays a trap that sacrifices hundreds of his own men in order to kill a god.
I'd put both of them in the villain category. Before the battle, I wouldn't put either of them in that category, but the climax really makes them out to be awful people. Eboshi in particular hides behind smiles and buying up the contracts of prostitutes (to make them her slaves) and helping lepers until the climax when she completely abandons them, throwing them to the wolves in service of money.
She has made a somewhat Faustian bargain with the other warlords and by extension the emperor. She is very different than them in caring for outcasts, but the state is still the source of her power, so when the emperor wants the deer-god's head she goes hunting, thinking quite naturally that this is the best she can do for her outcast villagers. Money for the village's needs (they are far from self-sufficient), the emperor's favor, and (as far as she knows) an end to god-attacks on the village? Of course she goes. The villagers are equipped to deal with more short-term threats, she made sure of that.
She is absolutely a non-evil, non-villainous antagonist.