3. Killing Zod
The Problem You knew this was coming. And before you run to the comments to tell me that this is a different Superman or that Im stuck in the Silver Age mentality or that Superman has killed in the comics, Ive heard all those arguments before. And they dont matter to me. The times when Superman has killed in the comics has almost always been as a result of bad writing and not a valid character choice. The biggest problem about the death of Zod is that its the culmination of all this reckless destruction Superman has helped cause without any regard for the ramifications.
The Fix Surprisingly, Im not going to say that Superman shouldnt have killed Zod at all. Rather, Im going to take the same approach that comic writer Mark Waid took: show Superman struggle. Have Zod push him to his limits. The revelation that Superman cares more for humans than Kryptonians should have happened earlier in the fight and should have changed that entire final battle. Instead of it being a direct slug-fest, Zod should have gone off on a rampage, tossing people from ridiculous heights, causing massive explosions, taking down buildings, and then show Superman trying his best to keep up, using his powers to try and save people and contain the damage. Lead up to the kill, and then it would have been easier to swallow.