I don't know, I think the Wachowskis could do the Justice League movie... ummm... justice. They have comic writing and graphic novel movie experience and understand the genre. The Neo/Smith fight in Revolutions was essentially a Superman vs an equally powerful being fight with massive side effects.
Sure, they can do the fights; that's not the issue. All the splashy action in the world won't make a superhero movie effective unless the characters are solid and engaging and the plot is reasonably coherent -- unless we care about why they're fighting.