I think the movie could have been streamlined a lot. I think Wonder Woman did play a role in the plot, but there shouldn't have been any direct references to any other heroes. Just put Justice League off for another six month, and lock down a Flash & Green Lantern Team up movie that would come out before JL. Aquaman could be teased in Wonder Woman's solo movie, and Cyborg can wait till JL to be introduced.

Second thing is I think the country where Superman has his international controversy, and the country where kryptonite is found should be the same freaking country. I know it would be a stretch for an island in the middle of nowhere to be the center of an international controversy, but we can fudge the geography a little, and the fact that they have a World Engine crashed on their shore would surly make them a bit of a hotbed.

I recommend that Lois is there to investigate their recent advancements in WMDs, and how it might be connected to the world engine. This would largely replace Lois's hunt for the magic bullet, and instead she would find out that Lex has been trading them weapons in exchange for kryptonite. I'd say we could actually have Superman's first run in with kryptonite be on that island, and at the time it would be played off as coincidental that he happened to be exposed to a kryptonite deposit while he's there, but later it would be revealed that Lex already know about the weakness, and had planed for Superman to be exposed to it at that time. That would however be the first time Superman, or Batman learned about kryptonite.

Finally the movie didn't freaking need Doomsday. I guess they needed him if they wanted to kill Superman, but that didn't need to happen either. There needs to be something to bring Batman, and Superman together after they fight, but I don't think it needed to be a big punchy villain. Instead I think they should have looked back at the White Portuguese plot, and made it a double twist. Batman was so focused on getting something to take Superman down that he accidentally did let someone smuggle a big freaking bomb into Gotham. Then Batman can go off to save Mrs Kent like he did in the movie, but Superman will have to split off to get rid of the bomb. He probably flies it into space so we can still get that cool sunrise scene.

The only real downside to no Doomsday is that it doesn't give Wonder Woman anything to do in the movie. She'd be getting her own solo soon though so I don't think that's too big of a deal. She'd basically just be in this movie as a plot device that increases Batman's resolve to take down Superman. He can't have the metahumans destroying another city in a fight with each other, or worse they might team up. With no big villain to fight she'd pretty much just show up at the end after the action, and the three of them would do a trinity pose.