Soon I Will Be Invincible by Austin Grossman

Soon I Will be Invincible (Vintage)is a straight-up superhero novel, narrated by Dr. Impossible, who breaks out of prison to enact his latest plan to take over the world, and Fatale, a recruit in the Justice League New Champions who vow to stop him.  In addition to fantastic inventions, origin stories, and epic battles, we also get insight into the psyches of these two.  Although they are on opposite sides their journeys are quite similar; both struggle to fit in and come to terms with their public and private personae.  It's this aspect of the novel that appears to be influenced by Alan Moore's Watchmen, although Grossman's story is far kinder, quite poignant in its depiction of lonely, regretful, mixed-up metahumans.

It's also a lot funnier. Dr. Impossible in particular is a delight, who manages to be egotistical, humble, neurotic, sardonic, and genre-savvy all at the same time.  He is obsessed with not only taking over the world but also with what constitutes his real self -- the dastardly supervillain and evil genius, or the lonely, invisible nerd. Which makes the climax all the more spectacularly ironic, because Dr. Impossible is just as guilty of not seeing past a costume or a power.  Turns out, metahumans are people, too.