Theory time.

All of a Sudden we have two Organizations introduced into a Pokemon Game, both seemingly being "Black and White", Good vs Evil, Order vs. Chaos.
We expect Skull to be the underdogs in the scenario and expect Aether to come out as the Main Villains of the game, my theory is that both are actually pawns in the Grand Scheme of one particular new Character.

>Smart enough to use Pokeballs.
>Able to command Pokemon to use moves.
>Able to use common items(Battle Items).
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>Team Skull is represented with Black.
>Black is often portrayed as Purple when needed.
>Guzma has both a Purple Tattoo and "Gold" Glasses.
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>The Aether Foundation is lead by Lusamine, who wears a White dress, stockings, and has both a star shaped crystal and Gold secondary color theme to her design.
>Lusamine loves all Pokémon loves all Pokemon, especially an "Peaceful" Oranguru.
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>Oranguru has clean and fixed White fur(Lusamine/Aether), and a Purple Coat that is wild and unruly(Guzma/Skull).
>Oranguru has a golden star shape on it's head(The common color between Lusamine and Guzma)
>Oranguru also has Light Orange and Purple lines going through it's Purple coat. (Orange=Sun/Purple=Moon).