I was just thinking a thread like this would be good!
I have to quibble with the note that Pokemon usually hides its villains at first. Cyrus, Lysandre, and Archie/Maxie were all hit-you-over-the-head obvious. Probably the best example of a hidden big bad was Ghetsis, and that was still pretty predictable from his design, but they at least positioned N to be the villain of sorts at the start.
Usually Pokemon villains tip themselves off by saying something dark and dogmatic about the world needing fixing. The Aether Foundation has been described in terms like, just going down their page: "[their] goal is to care for Pokemon that are hurt", "provide shelter", "research", "lovely", "caring personality", and again, "shelter and care". Even a "Foundation" calls to mind charities. If I try really hard I can read something a little too magnanimous in Lusamine's "worthy of my love" comment, but I think that's a stretch. Pokemon doesn't want to assign villainous motivation to things like love, shelter, research (Pokemon is all about research, really), and charity. They don't want the message of a game to be "people who really want to help animals aren't to be trusted." Unless in practice, they're like Plasma and are separating those Pokemon from their habitats and trainers, but we haven't seen evidence of that yet.
All that said, their floating artificial "paradise" is kinda creepy, Faba looks like Faba, and their musical theme is electronic and neutral. We can guess there's something more going on with the plot, if only because of all the moving parts. The biggest indicator to me is Gladion -- he has that anime antihero look, and if the theory that he, Lillie, and Lusamine are all siblings is correct, then the fact that he defected to the villain side with a weird legendary suggests the Aether Foundation did something objectionable in its past, perhaps creating Type: Null or the UBs. Somebody has to tie up all the alchemy threads Pokemon's been spinning recently. And the grunts and multiple branches of Aether create the possibility that a branch could go rogue and you have to take them on. But I really doubt the story takeaway will be "Yup, Lusamine and Wicke and their motivations are just evil! Gotcha!"
After BW and XY, I'm guessing GameFreak heard the story praise for Gen 5 and widespread criticism for 6. XY was a really monumental effort to bring the series to 3D, but story fell by the wayside. I hope they see that, and aspire to get back to a more fleshed out plot in this second 3DS gen, making XY a style over substance outlier rather than the new norm for the series. All the elements are there, but if Gladion and Plumeria and co. turn out to be one-note villain encounters and little more, like Xerosic and the Flare admins, I'll be sad.