Flare was pretty transparently evil
Aether is most similar to Galactic, whose cover story was betterment of man kind. Though in that case, the rank & file weren't aware of Cyrus' true goal and how it'd entail.
Assuming Aether isn't explicitly evil, I can see it being a thing like "we're doing this secret bad thing that involves chimera experiements because its the only way* to save the world/pokemon"
*not actually only way, shortsighted, follies of man, blah blah blah
I also wouldn't be surprised if Lusamine isn't privvy to the underbelly of aether mostly because Faba is so very clearly a mad scientist who would be doing his own thing i mean look at him
He reminds me of Blaine for some reason. I guess good ol' Oak isn't the only one to have a cousin in Alola.