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Let's do some autistic "fix the story" with this place. I'll start
>Learn about it through the library while Lillie is researching stuff
>First possible encounter is optional and can get you a cutscene or something
>Mandatory after Po Town, change the script to have Aether grunts researching the lake, find Lillie, and steal Cosmog (having team Skull steal it was stupid)
>infiltrate Aether Paradise like normal, Nebby becomes Cosmeom, bla bla bla
>find out Team Aether is guarding the lake, forcing you to find the Altar on Poni
And this is just off the top of my head to get the discussion going on. I'm sure it would be able to fit better after a few revisions