This. I'd hope for something incredibly cultish. Perhaps a cult obsessed with purity, and the other with chaos or corruption and they switch around as antagonists like Aqua and Magma in Ruby and Saphire. The Order of Lumis and The Umber Syndicate. That would fit with the light/darkness theme but it's a little over the top, evern more so than Team Galactic and their new universe idea.. I just hope they don't go for a "gain-control-of-the-legendary-and-use-it-for-our-evil-purpose-mwah-ha-ha-ha-ha-look-at-how-evil-we-are-we-are-so-evil-bet-you-can't-defeat-our-zubats-and-stop-us"-esque plotline again as it's no longer original.
That brings me to my other point. Will the evil teams please STOP USING ZUBAT!!!! It's getting really old now!