This year, we have had two movies that explore conflict between superheroes, with DC/Warner's entry into the series, Batman vs. Superman, and Marvel Studios' entry, Captain America: Civil War.
The latter does a better job exploring the depths of this arc than the former does, finding a good mix of lighthearted material with more somber moments that cause one to reflect about who is really right or wrong in the debate between Captain America and Iron Man.
Spoilers come after the link, so don't read any further if you haven't seen the film yet and don't want to know what happens.
The gist of Civil War is that the United Nations has become concerned about the ramifications of The Avengers and the action they have taken to save the world, but at a cost of some innocent lives; the latest when The Avengers try to stop Brock Rumlow from stealing a biological weapon. Rumlow sets off a bomb, attempting to kill himself, Captain America and a number of bystanders, but the Scarlet Witch manages to levitate Rumlow into the air, only for the bomb to explode near a building, thus killing other bystanders.
The United Nations is set to pass the Sokovia Accords, under which The Avengers would operate under the direction of the UN. Tony Stark, aka Iron Man, is on board with the idea because his creation of Ultron led to Sokovia's devastation (and is further influenced by a mother's story about her son being killed in Sokovia while on a humanitarian mission). Steve Rogers, aka Captain America, is unwilling to sign, given his past history with working for SHIELD and how its direction had been partly influenced by Hydra's infiltration.
This sets up the conflict between Rogers and Stark, in which each superhero has valid reasons for picking a side and neither one ever comes off as the villian, although each could be thought of as misguided in certain ways. The conflict becomes greater when Bucky Barnes, aka The Winter Soldier, is blamed for a terrorist attack in Vienna where the accords are to be signed (an incident that leads to the death of King T'Chaka of Wakanda, leaving his son T'Challa grieving and in pursuit of Barnes).
Rogers tracks down Barnes to Bucharest and learns he wasn't in Vienna at the time of the attack, but he, Barnes, T'Challa and Sam Wilson (aka The Falcon) are eventually captured after leading authorities on a chase in Bucharest that endangers more people. They are taken to Berlin, where Stark convinces Rogers to sign the Accords in exchange for a pardon, only for Rogers to refuse once he learns Stark has confined Scarlet Witch (Wanda Maximoff) to Avengers headquarters and won't allow her to leave for any reason.
Stark takes the role as one antagonist, the rare type who really isn't a villian but has legitimate views that conflict with other legitimate views of the protagonist (Rogers). This especially comes to a head with the final confrontation between Stark and Rogers, in which Stark learns an uncomfortable truth about the death of his parents and Barnes' involvement.
There's another antagonist as well: Helmut Zemo, a resident of Sokovia whose family was killed in the devastation and has set out to divide The Avengers by researching Hydra's work with The Winter Soldier. Zemo isn't your typical villian; he has legitimate reasons for being upset with The Avengers, but his tactics can be called into question.
The movie also does a wonderful job introducing movie goers to T'Challa, aka The Black Panther. He becomes a sympathetic character just moments into the film and goes through a dynamic character arc, from a man who is seeking vengeance for his father's death to a man who realizes that vengeance isn't always the right path.
Oh, and then there's Spider-Man, a younger version of the superhero who steals the show during the major fight scene between the conflicting superhero teams. Spider-Man represents just about every comic book geek out there -- he can't help but be in awe of the likes of Captain America, even as he's supposed to be working on behalf of Tony Stark.
There are a lot of elements and characters to sort out in the film but everyone of the superheroes gets a cool moment. More importantly, the storyline doesn't make anybody to come out as "the bad guy," with only Zemo's actions being called into question. People can relate to Rogers, Stark, T'Challa, the United Nations' position -- none of them are outright called someone in the right or in the wrong on every point, nor does the film conclude that any of their positions are the correct position.
Compare that to Batman v Superman, which tries to set up a conflict between the two superheroes but doesn't execute it well. BvS was a flimsy attempt to set up a showdown that doesn't really allow people to ask themselves whether it was Batman or Superman in the right and seems more concerned about building to a fight between them for the sake of it. Additionally, BvS tries to do a lot of things but isn't as effective at tying everything together.
Civil War ranks in my top five Marvel Studios films and makes me want to see more of the upcoming films. Most of all, the directors and writers understood how to put superheroes in conflict without definitively making them "all right" or "all wrong."