Noxus: 
(Might change in his new lore)
Zaun: 
Shurima: 
The void: 
Bilgewater: 
The Shadow Isles: 
Ionia: 
Frejljord: 
Piltover and Demacia doesn't have any straight up "evil" characters. But they do have champions with questionable morals such as 
and 
.
For Ionia, I have to disagree with Jhin. He's certainly the most evil Ionian character, but from a story perspective he isn't the most antagonistic to a majority of Ionian champions.
That would be Zed and, by extension, Kayn. Jhin's completely evil and needs to be stopped, but he's just one person. Zed has a full following.
Demacia has it's antagonists, they are not from Demacia themselves but still, 
and 
each of them attacked demacians in their respective lores.
Evelynn made a cult of herself in the mountains of Demacia and fed on her believers (Quoted in new Vayne's lore), she ignored the anti-magic walls and killed many great nobles.
And we forget "non-located/situated" villains and antagonists such as 
and OF COURSE, and
I can't decide between Singed and Urgot when it comes to Zaun. While Urgot is planning to throw Zaun into chaos and anarchy, Singed has a pretty bad effect on Zaun as well. He is the reason Warwick exists in the first place and helped Noxus attacking Ionia with poison gas.
They both qualify as the main antagonist in different senses in my eyes. Urgot more like the evil monster lurking in the depth. Singed as the evil mastermind who was controlling Zauns fate in the past and actively leading to make it the hell it is today.
And like someone already mentioned, Zed is a better candidate in my opinion than Jhin for Ionia. The rest, I agree with. But your thread shows something I thought for a long time myself: Piltover could use a champion on the evil side of the spectrum.
Although Viktor is more so a protagonist and from Zaun, I could see him as the main antagonist currently for Piltover. Pilties seem to love to hate Viktor.
I would disagree with Cho though. I don't think we know too much about his status as a Void creature, how powerful and what his ranking would be in comparison to other void creatures. Not to mention his intelligence isn't really known, unlike Velkoz is is supremely knowledgeable.
I don't think there's antagonists or protagonists in league really. The only antagonists I can imagine are those that want complete destruction of the world or something. People with ideals like Zed, Swain, Gangplank, and Urgot to a lesser extent, I would not call antagonists.
Well, technically, Swain is not the antagonist of Noxus
Swain is the antagonist of Demacia, and Jarvan would be the antagonist of Noxus.
Also 
A place of evil, like the Void, doesn't have an antagonist considering that the entire plane itself is the antagonist to Runterra as a whole.
I also disagree with quite a few of your selections.
Swain isn't the antagonist in Noxus. He's their Grand General, the military leader of the nation. Why would he be in opposition to his own country? If anything, Mordekaiser is the main, shadow antagonist of Noxus because the city is built upon his impenetrable castle that he wants back in his possession. Otherwise, Noxus is pretty much trying to conquer everywhere else, so most of Runterra is antagonistic to Noxus.
Zaun also doesn't have an antagonist, other than Piltover. The city is built on free thinking chaos and crime. Urgot is only creating an uprising there to build the army he needs to take vengeance on Noxus for imprisoning him in the mines. There is no central antagonist to a city of crime because it exists in such chaos that the only thing to oppose it is Piltover.
The Shadow Isles, likewise, are too chaotic and wild to have a single protagonist. Mordekaiser is trying to subjugate it, but he can only do so much, and he isn't trying to outwards destroy the place. Their main antagonists are Yorick and Maokai, the last living inhabitants of the Blessed Isles who seek to undo the undeath and return the islands to their former glory.
Bilgewater, again, like everything above, is chaos. There is no main good force there so there is no main bad force. It is all pirates and vagabonds fighting for power. Gangplank is just as much a contender as Miss Fortune.
Lastly, if you intended to discuss characters from regions with darker sides, that's completely different than an antagonist. An antagonist opposes a protagonist. Darius and Garen are antagonists and protagonists for each other for their respective nations. There are many instances of this. Someone like Vayne is just a dark character, she isn't an antagonist of Demacia, but she does have antagonists in every form of evil and dark magic in the world, especially Evelynn.
