A plague seems like a good fit for Kanto to me. What's the alternative? Reviving Team Rocket? A new villainous team?
I can even see how it might be tied into the Mewtwo-Mew story. What if Fuji created Mewtwo not for the sake of science or power (which wouldn't be consistent with his benevolence), but for the purposes of developing a cure to a previous plague that took the lives of Guyana Pokemon (and maybe even people)? And tragically, the plan never came into fruition since Mewtwo escaped? Wouldn't it be heroic justice if many years later, Mewtwo finally fulfilled its purpose, albeit under different circumstances?
The idea is that if Mewtwo is strong enough to survive a virus, then its body should be able to develop an antivirus. This sounds simple, but the plot could become complicated for two reasons:
1. Fuji is no longer alive to share his knowledge.
2. Mewtwo's trust needs to be gained.
I can see Lusamine being instrumental in unearthing Fuji's research, and Lillie being the key to communicating with Mewtwo. Moral questions would be raised as to whether or not Fuji was justified in "horrifically" splicing Mewtwo's genes to save others.
I can even see how it might be tied into the Mewtwo-Mew story. What if Fuji created Mewtwo not for the sake of science or power (which wouldn't be consistent with his benevolence), but for the purposes of developing a cure to a previous plague that took the lives of Guyana Pokemon (and maybe even people)? And tragically, the plan never came into fruition since Mewtwo escaped? Wouldn't it be heroic justice if many years later, Mewtwo finally fulfilled its purpose, albeit under different circumstances?
The idea is that if Mewtwo is strong enough to survive a virus, then its body should be able to develop an antivirus. This sounds simple, but the plot could become complicated for two reasons:
1. Fuji is no longer alive to share his knowledge.
2. Mewtwo's trust needs to be gained.
I can see Lusamine being instrumental in unearthing Fuji's research, and Lillie being the key to communicating with Mewtwo. Moral questions would be raised as to whether or not Fuji was justified in "horrifically" splicing Mewtwo's genes to save others.
I suppose that's true, about Necrozma. UBs as the threat again would be somewhat redundant - it just seemed like an convenient way to get Mewtwo involved as a protector.
I do still think the plague idea would be interesting and innovative (at this point though, I'd love to see any kind of non-Trainer or non-Pokémon antagonistic force*), but I dunno, I think if I had the choice, I'd prefer to see it done in a new region rather than Kanto. Were it to be in Kanto, however, then having Lusamine be the source of a new virus seems like a logical opening for it - we really don't know what else her merger with UB-01 may have done to her. And it gives her a route of atonement, if she chooses to take it. She certainly has the money and resources to research and attempt to produce a cure or vaccine. It'd help to restore the Aether Foundation's image, as well.
* I know that the Delta Episode is sort of similar to what I'm looking for in a more abstract antagonist, and I did like that, but the meteor was only the threat for the duration of a post-game plot, so it's not quite what I'm wanting.