I would also pull up the lovecraftean overtones of gotham that rear it's heads from time to time.
Afterall, Wonder Woman vs Cthulhu is guaranteed to put butts in seat, especially if she puts together a team of Nightwing, Spoiler, Batgirl (Cassandra Cain), Oracle (you could use the temptation of walking as a major plot point), Bane (the things he'll do for love as he's become the Catwoman analogue), Mr. Freeze, Jason Blood and Zatanna.
vs
a Lovecraftean Joker (he became it's avatar as a joke and the Joker gangs are his acolytes, led by the mad priestess Harley Quinn), Maxie Zeus (it's a father always loved her best issue), Scarecrow (he loves the fear as he's a Phobos bastard), Clayface, Doctor Psycho (because that horrid little man is one of her best villains, and a mad psychic fits the tropes), Killer Croc (mostly going along for the ride, but he's been infused with dark stuff and is Bane's personal enemy after what he did to the batclan and his own personal honor).
Monsters used: Animated dead, Byakhee, Color out of Space, Deep Ones (in gotham harbor), Dhole (because a big ass worm fight in the middle of Gotham would put butts in seats), Ghouls (they have been feeding in the cemetary, the streets and the asylum), Gugs, Hound of Tindalos, Nightgaunt, Shoggoth, Leng Spider, Star Vampires.
Neutrals: Penguin (he just wants to make money), Poison Ivy (she could very easily go either way), Maxima (she has her own agenda and I've always believed she would make an awesome foil for Wonder Woman). Veronica Cale (while she hates wonder woman, she's her own woman), Raj Al Ghul (he wants Gotham to burn, but it's to put out the Lovecraftean horror before it reaches full power and he's the most aware of what they are up against, plus Bane/Raj interaction always is a draw). Two-face (he's been chosen as the avatar of Janus after his disorder and it's a total coin flip whether he helps or harms).
Nora redone as a lovecraftean horror after being "save" would give mr freeze a spatterhouse feel to the character that has it's own ability to draw stories.
and of course Ares is thriving on the violence as he feeds the flames.
Plus I would take a page from the Grimm TV show and make a few classically Greek races and monsters and hide them in plain site. The two big ones are Gorgans and Minotaurs, but I'm sure there are others. Besides dealing with eldritch horrors, wonder woman and co would also have to deal with "the monstrous in everyday life" as they act as mediators between the various factions that are just trying to live their lives within the city.
Plus the Asylum is where we get to see both the heroes and the villains at their worst. Just about everybody gets a breakdown now and then and while it's their best hope for keeping their sanity, it's not pretty.
I think such an environment could drive stories for decades. :)
