I felt that the movie should have been broken up into a 3 movie system, much like the Nolan Batman trilogy.
Warning: Spoiler! (Click to show)
Movie 1 could focus on Krypton, Zod background, the Krypton battle, Superma landing on earth, childhood, discovering his powers, adulthood, and then ending when he discovered the large spaceship - sees his father/Krypton blows up and we know that the prisoners are free.
Movie 2 could focus on Superman continuing to hone his powers, build up the lover interest with Lois, have Supe discover more about Zod and his homeland, have Zod go free and discover the world engine, end with "You are not alone" - with Supe getting "arrested".
Movie 3 would be the big battle, fighting against then fighting with the humans, showing him saving (and actually caring) about humans, engage in battle with the Zod crew, destroy World engine, destroy Zod - we now finally have our "Man of Steel"
Trying to cram all of that into a single movie just proved confusing, jumpy, and bizarre. It felt like there were hours left on the editors floor, since some of the gaps were incredibly bizarre. Here's to hoping there is a 2.5/3 hour edit that will eventually come out in the future.