Two alliances of villains:
The first group is the Legion (of Doom, but don't focus on that.) Formed as a reaction against the Justice League, this group contains mostly heavy hitting immortals wishing to maintain their status quo and even overtake the League and outright rule the world (OF COURSE!) via their use and control over dozens of smaller villains. Their leaders are mostly classic Big Bad types; while they are dangerous in personal confrontations, they prefer to have others do the dirty work.
Lords of the Legion:
Ares: Theoretically the most powerful member, being a god of war and all, but needs out-and-out conflict to maintain his power, and the cause for the Legion's more public menace.
Circe: Ares' lover and a demigoddess in her own right, she joins the Legion specifically to continue fighting Wonder Woman, and her powers are stable, unlike Ares's. Therefore, though he is capable of more impressive feats, she's normally the Legion's heaviest gun.
Vandal Savage: The single most durable member; he can't be sealed into Tartarus like Ares or Circe, and will return from even a single cell. Sees this as an opportunity to assume leadership over all mortals and is thus the main long term strategist of the group. Has been a hero and villain throughout time, and has actually forgotten whole stretches of history due to his immortality.
Ra's Al Ghul: Youngest and least supernatural member of the group, he nonetheless commands the largest material forces of the Legion. Sees the pagan gods as temporary allies who will fade into myth soon anyway, and believes Savage will simply flip into another belief system anyway, which would leave him as their most stable member and practical leader of the Legion.
Abra Kadabra: Time traveler and master of both magic and technology. Seeks to have as much fun as possible fighting superheroes.
Their lieutenants and henchmen:
Lex Luthor (that's what he wants them to think)
Parasite (usually dumb, but can get very clever after feeding)
Sonar (a thug designed to counter Green Lantern)
Cheetah (friend of Diana Prince turned enemy by Circe)
Ocean Master (he wants to broker a deal to protect Atlantis)
Unknown assorted villains. They are Legion, after all.
Then, Lex pulls off a coup. He worked with the Legion to ensure both they (as his rivals) and the League (as his targets) would wound one another and allow him to fill in the power vacuum. His new organization, the Secret Society, deliberately seeks to confuse their numbers and operations, and they have recruits and allies who the can activate from unexpected areas.
The Light, leaders of the Secret Society:
Lex Luthor: Unofficial head and main planner because he knows and they know he eventually plans to betray them and likewise, but he's still the best at his job. Mostly detached and coolly calm about the League, with the one exception of his obsession with not just killing Superman, but destroying them. Only member of the Light to still have a public life; he uses the good publicity he has as a cover.
Bane: Highly ambitious and vicious, recruited into Luthor's conspiracy to incapacitate Ra's Al Ghul. A tactical field leader, he commands his own private army and prepares for a showdown with Luthor as well.
Talia Al Ghul: Luthor's double agent in the Legion's Lords, she turns on them at the opportune moment and reforms the Demon into Leviathan. She mostly seeks to avenge herself on those who have wronged her and erect a new world order for her son, Damian Wayne.
Cheetah: Being created by Circe's magic and backed up by her own studies, takes down Circe and seeks to gain enough magical power to both keep her powers and live a normal life when she wants to.
Zoom: Flash's personal enemy. Has an understanding with his colleagues that the Flash is his to deal with, not theirs.
Sinestro: The Light's big gun, allied with Luthor to gain a foothold in Sector 2814 for his Sinestro Corps in preparation for Darkseid's invasion of the dimension.
Their henchmen are sleeper agents like Superboy, Terra, and the Tomorrow Woman, while their overt henchmen are the Royal Flush Gang.
And when this group inevitably falls on itself as well, Luthor gives the Royal Flush Gang to the Joker and hits the deck.