The thing is, Superman can't be morally ambiguous. The moment he starts to compromise his beliefs and values, is the moment he starts to go down a path he will not be able to pull himself away from, and God help the poor mortals who try to stop him. Crossing the line and killing Zod removes the line. It opens the door for him to compromise his morals each time he's up against a "no win situation."
It's actually Batman's greatest fear in the movie, and Superman literally does NOTHING to dispel those worries. The conflict between the two doesn't end because Superman manages to prove to Batman that he isn't a monster. It ends because their mothers share the same fucking name. I mean, Jesus Christ is that awful.
The whole point of Superman is that he is a nigh unstoppable God, yet due to his stellar upbringing from the Kents, who are honest, Noble, genuine, and selfless people, Clark grows up to become a great man. He understands and respects the burden of his powers, but he has a rock solid moral compass. He's not perfect, of course, and he's often challenged and tempted to take the easy path to solving his problems, because, well, his powers allow him to do such things, but he will never take that easy path if it's not the right path. The right way isn't often clear cut, so he chooses the path that will result in the least amount of harm to come to humanity.
How Superman manages to maintain his morality and integrity while dealing with foes that will commit atrocities with no compunction, is what makes him an interesting, compelling character. When he's up against a no win scenario, and he comes out on top, you cheer. Superman isn't boring because he's good, or a Boy Scout. Superman is boring when writers don't understand why he's such a complex character. I'm actually not a big Superman fan. I don't hate him, but I like him when he's done well, like in the Superman Animated series, and comic storylines like All Star Superman and For All Seasons to name only two.
Superman moping about his place in the world for two whole movies isn't interesting, deep, or emotionally stirring. It could be, for a first to second act in a single film, but by BvS, he should have been a beacon that humanity rally's behind. The problem is really that BvS is a movie tha we should have gotten after Man of Steel 2, Wonder Woman, Batman, Dawn of Justice, and Justice League 1. It's a story that wasn't earned in any capacity. The world's reaction to the battle of Metropolis is enough meat for the entirety of Man of Steel 2. WW and Batman solo films would have been able to establish both characters and their mindsets and motives, Dawn of Justice could have been the trinity coming together, and setting out to find the other meta humans, and dealing with a threat tha would require all three, while hinting at a threat that perhaps the three of them aren't enough to handle, thus cementing the need for a Justice League.
The JL movie would be the payoff, and maybe another sequel, one that lays the groundwork for a rift in the relationship between Batman, Superman, and Wonder Woman. Maybe the death of Maxwell Lord and Ted Kord causes friction.
Then, you give us Batman v Superman. By that point, relationships have been established, friendships built, and tension is at its highest. You can put all the Dark Knight Returns imagery and fan service you want in that film, and it'd have felt earned. Sure, it may have taken 8 years to get there, but fuck would it have been worth it. Maybe cap off the whole thing with a Doomsday movie after BvS.
But no, Warner/DC wanted that Marvel money, but they didn't want to do the work to get there. They wanted to short cut their way to Avengers style profit, failing to realize that Avengers worked because, even though the stories for both films are average at best, audiences were all on board because the cast is so damn personable and likable. It's not the quips or the light tone, it's that Tony, Steve, Thor, Hulk, Widow, Hawkeye and the rest are relatable characters. They act like human beings, not living action figures being mashed together like a kid playing. Would you want to have a beer with Superman or Batman? Fuck no. But I'm sure most of us would hang with Steve or Natasha at a bar.
I'm a huge DC and Marvel fan. I grew up loving their characters. What we've gotten on the big screen with MoS and BvS are poor imitations of those characters. Arguably the most iconic characters in comics, and audiences aren't resonating with them because they don't really feel like them. Affleck was a solid Batman, but all we get of him in this movie is the obsessed Bruce and brutal Batman. There's not much humanity to buoy that rage, and it makes him feel distant and removed from us. Not very empathetic. The best Bruce/Batman scene in the entire movie isn't the warehouse scene where he goes all Arkham video games on us. It's the scene at the very beginning, where Bruce is witnessing the battle between Clark and Zod, and the buildings are coming down, and people are dying, and we see Bruce actually behaving like a human being and being a hero. The rest of the movie is downhill for every character after that scene.
I haven't written off the DC Cinematic Universe yet, however. I just don't think it needs to take three movies to get characters on the screen that resemble their iconic and heroic comic counterparts.