Spoilers still:
I don't take Superman's killing of Zod to be a big character change so much as it is part of the character which is incredibly rare. Superman once executed 3 rogue Kryptonian criminals (including a version of Zod) in the Pocket Universe story from the late 80s. It was a heavy burden but there was no choice in the matter. Similarly, Superman battled Doomsday knowing that he would have to kill him in order to stop him, which he did. (Of course Doomsday took Superman's life as well.)
I compare this positively with Superman II, where Superman casually tosses the de-powered Zod down a chasm, knowing he will fall to his death. In MOS, Superman pleads with Zod to stop, and then he is clearly emotionally devastated by what he had to do in that situation. The end of Superman II alway seemed incongruous to me.
I'll agree with the nitpicks -- couldn't he had covered Zod's eyes, or flown away? -- but as it stands I like the scene. As I said on a G+ comment, it's a harsh character beat but a legitimate one.
As far as the cast, I might be on my own but I really liked Kevin Costner as Jonathan Kent. He has the sort of stoic fathering approach which I would expect from a Middle America farmer like Jonathan. I get the feeling that Jonathan has a hard time expressing his love for Clark, as I imagine that nuturing fathering is something he did not grow up with. The only time that stoic facade is broken is in the barn with the ship, "You are my son."
I LOVED the anti-Donner vision of Krypton. Reminded me of something from Edgar Rice Burroughs. Crowe was great as Jor-El, which helps those scene as well.
Did anyone else assume that the large Phantom Zoner who fought Superman with Faora was Non? Because I did!
Easter Eggs -- besides the Lexcorp ones (a Lexcorp truck in Smallville, made me think of the show Smallville, heh), the satelite has a Wayne Tech logo on it. Supposedly when Jor-El's program is showing Superman how he came to Earth, there are two ships -- and supposedly the Walmart prologue comic suggests that this is Supergirl, as a set up for the sequel. Also, the scientist of the Phantom Zoners is credited as Jax-Ur, who was a PZer in the comics.
Looking forward, I want Brainiac in the sequel. Either use the Kryptonian tech like Edward suggested (which was put to great use in the DCAU), or avoid the Kryptonian connection altogether and use the modern Colun style, with his army of drones and all of the bottle cities, come to Earth to capture the Last Kryptonian (sort of like we saw in Superman Unbound). Couple that with Lex Luthor and his team of armored personal security as a sort of third party. For the third film I would use Doomsday -- with all of Zod and Faora's talk of evolution breeding superiority, Doomsday is a no-brainer; his origin as a Kryptonian experiment in forced evolution fits perfectly. Just do Doomsday from the comics, replacing the Justice League with the Metropolis SCU and Lex's crew. This sets up the fourth movie as well!