Let's get the movie's problems out of the way.
Firstly, there's a serious lack of connective tissue. The whole first half is basically one abrupt transition between awesome moments after another. This doesn't really let up until the title fight. I think that the extended cut could solve a ton of these problems. So many scenes are like 30-45 seconds from greatness. There's also one or two scenes that really should be present but aren't; we need a scene where somebody lays out why people are wondering if Superman is responsible for the deaths following the massacre, and one detailing Lex's reaction to his exposure to the archive. If they turn up as well we're looking at a Kingdom of Heaven-esque turnaround. As is, I can see why a lot of people are frustrated. This is a movie that not only refuses to hold your hand, it straight up makes you do a lot of connecting the dots on your own.
Second, the soundtrack. One thing I didn't realize is that it's all very, very dark sounding. There really isn't an uplifting, triumphant sound in there. No lighthearted music. It ended up making scenes that are clearly supposed to be lighter in tone feel much darker, one early one in particular stands out. The thing with the African warlord who had Lois; you're clearly supposed to be going "oh shit it's Superman, here to save the day!", but the music says "oh no things are about to be bad!"
Now, the rest of the movie. There's a major misconception I keep seeing that I need to refute: this is not a cynical piece. It simply isn't. It's a refutation of Batman's speech from the trailer, about how there are no good men. It's a denial of the idea that his behavior, his callousness, the branding thing, that that's acceptable. That we must live as if perched on the edge of Armageddon. This is accomplished through Clark. You see how his doubts and uncertainty surround him, suppress him. Make him wonder if what he's doing is really the right thing, if there
is a right thing. But then he comes back. He comes back because god dammit, the world needs heroes. It needs good people. And good people don't need to live charmed lives.
And that's what the movie is about. That life is going to kick you in the teeth, make a mockery of your efforts, but that that's not the end of it. That you can overcome, be more than you are. Be better than you are. And it delivers on those ideas in a big way.
I get why the disjointed front half would put some people off, make them stop paying attention and miss the message, but if you can keep on it, this is one hell of a film.
Wait, so Batman has a nightmare about Superman, but Flash time-travels from the future into Batman's dream?
This is what I'm talking about. Connective tissue. if the Nightmare starts with Bruce spasming a little bit, maybe some weird screen effects, it becomes obvious that it's not a normal dream. Because duh, it's not. But it needs to be made a little more clear.