Marvel has its own share of dark storylines. Very similar to DC's Injustice is the Civil War arc, which follows the clash between the members of the Avengers over how much power superheroes should have over the world. While Iron Man professes that governmental authority should be paramount, Captain America rebels against the authoritarian aspects of Iron Man's rhetoric. Heroes take sides and clash in a bitter conflict.
The stories of the X-Men are filled with conflict which challenges the viewer to think about social issues. In the world of the X-Men, humans fear those among them called mutants, born with genetic enhancements to their bodies and abilities. As a result, mutants find themselves under oppression from the government and society. While some mutants, like those under the leadership of Professor X, try to forge peace, others under the influence of Magneto decide to strike back in retaliation. These stories are filled with examinations of prejudice, acceptance, identity, and community. They depict fear, hatred, and ignorance in a very real and relatable way.
Those are just some examples of Marvel's dark storylines. Furthermore, "dark" need not always be better. A story can have a lighthearted tone and still teach valuable lessons. Marvel excels at this; while their movies are known for quippy humor and common plots, they still manage to teach valuable lessons through Iron Man overcoming trauma, Thor learning responsibility, and Star Lord discovering his family, along with many more examples.