Team skull being perceived as the evil team and the aether foundation actually being the evil team but it's for a different reason.
The Aether Foundation is feared among Alola. Not because of any cruel acts( however they may go unnoticed), but because of the sheer presence the Aether Foundation have. They have quickly built an entire island for themselves, as well as placing different facilities around Alola. They have eyes everywhere and it's been that way for a while. Generally, the Alolan people fear/ feel the pressure of the Aether Foundation, specifically things are mixed. There some that are are angered by them and are hoping that the Tapu's just smite them already. There are some that are completely neutral towards them. Some thing that they are good for Alola, giving them resources they didn't have before. And some, mostly elderly folk, who knows there's a problem and actively ignore it. Both in fear of what would happen if they did intervene, and also in having the mentality of " if we don't bother them, they don't bother us"..... despite the fact that said foundation is clearly taking more recourses than giving. It's a problem that has been plaguing Alola and they all come to a point of just accepting it and rolling with the punches. But for some people, that shouldn't be the case.
Enter Team Skull, the only people ballsy enough to actively go against the Aether Foundation. This could cause a change in events, as Guzma wouldn't necessarily be working with Lusamine. Maybe, idk, his big weakness is wanting acknowledgement for his strength, so who knows. In this story events, the people of Alola don't dislike Team Skull because they are just rowdy and annoying ( okay maybe a little) but because they are actively disturbing the "peace" between the Alolan people and The Aether Foundation. Especially the elderly people, who some ended up just accepting their circumstances and push for others to do them same.
This idea would also affect the characters. Hau would be affected and give him more reason to be more relaxed and happy go lucky, just to distract everyone ( and himself) from their situation. But that doesn't mean he isn't bothered by it, but his grandfather doesn't seem so bothered, nor do any other adults, so he just forces himself not to be bothered as well. It doesn't work.
Lillie and Gladion are interesting in that their mom is the one running the whole thing. I feel like them rubbing away is just a huge wake up call to how Alola is currently being treated. Like they very well know how cruel Lusamine is, given her abuse, but they never really thought about how she affected everyone else. This isn't to undermine their abuse!!!! That whole plotline is still a thing that will be addressed, and this is not for either Lillie or Gladion to go " man, I guess I got off lucky". No. Absolutely not. This is mostly to incorporate Alola's struggles more into the main game that just the Aether Family plot. Gladion joining Team Skull would also makes sense, as he is now actively going against his mother, instead of ending up joining a team that joined forces with the aether foundation.
Kukui building the pokemon league makes even more sense since it would be his way of fighting back. Subtly of course. If Alola has something to rely on that isn't just tourism and the Aether foundation for money and resources, they probably won't be as afraid ( tbh, I'm not sure if fear and afraid are the correct terms to use her, but I can't think of anything else) when it comes to the Aether Foundation. It still has it flaws and backlash, of course, but it's an Alola Original.
The protagonist is a bit harder, but the one idea I have is it going back to their mom. Maybe she ends up working for the Aether Foundation since she needs a job? Thus making the protagonist involved by default? Idk, but the protag is still there.
I also want to make it clear that the problems from the Aether foundation is more about how it's run and not every single person in the foundation. Like I believe they're done workers who genuinely want to help Alola! Some may be Alolan themselves, and want to see if they can change things from the inside. But with Lusamine and Faba at the top seats, it's very hard to do so. The end goal is for the Aether foundation to have less power than the already have. They can still exist and help Alola without having such power, you know?
Anyway, that's my idea. I hope you guys liked it!
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