All of these are really good ideas! I would love to see some of the sets made that people talk about. Although, I do have to agree that I just feel like Lego wouldn't touch the Arkham Asylum games or Christopher Nolan Batman film trilogy. So here we go as far as my ideas for sets.
DC UNIVERSE:
Birds of Prey Chase Truck, motorcycle, and street set-up(street light, garbage can, etc.) Includes Black Canary, Huntress, and 2 thugs
Justice League Headquarters Not sure if it should be the Watchtower or the Hall of Justice, but I would love either of them as long as it's got a round table for the founding members, control panel, landing dock with a Javelin. Includes Superman, Flash, Martian Manhunter, Hawkgirl, Grodd, Giganta, and Bizarro
Attack on the Hall of Doom The big screen with the podium, and the chairs with the U-shaped table. Includes Batman, Wonder Woman, Green Lantern, Lex Luthor, Cheetah, Scarecrow, and Sinestro
Brainiac Attack! An street resembling the front of the Daily Planet building. Includes Superman, Lois Lane, and Brainiac
Atlantis Under Siege! Something resembling Atlantis ruins. Includes Aquaman, Black Manta, and henchman
Grundy Break-Out A jail-cell with a blast wall and just a way to get a Green Arrow Includes Green Arrow and Solomon Grundy
I can only speak for DC. Marvel gets confusing because it's tough to in what direction? Do you stay Avengers? Spiderman? X-men? Fantastic 4? Like I dunno. All the ideas so far sound good!