Let me start by saying that I enjoyed the movie.
I adored Kevin Spacey's evil turn as Lex Luthor from the moment he appeared on screen in his first bad wig until he threatened to eat the dog. Kevin just knows how to be bad and to make shivers run down your spine.
Brandon Routh had just the right dorky charm to be Clark Kent and the body to fill that suit. He didn't need to be a Thespian. Superman isn't that much of a talker. Have you read his dialogue when he's battling crooks? "You'll never get away with this, Luthor!" doesn't take much acting ability. The ability to "wear the suit" instead of it wearing you and look adorably dorky are much better qualifications.
Kate Bosworth was not the Lois we expected, but she was the Lois for this story. She was a woman who had been left behind with a fragile human-alien hybrid child who had to learn to cope, who had to move on. Kate Bosworth might not have been Margot Kidder or even Teri Hatcher, but those women weren't who this Lois was.
James Marsden as the new man in Lois' life? He was good. He was heroic without being Superman. I loved how he started figuring out that Clark might be Superman.
Frank Langella as Perry White. That was inspired casting. He's played enough heavies that playing a newpaper editor with just a little bit of the tabloid journalist in his soul worked perfectly.
And who didn't know that Parker Posey's Kitty would betray Lex in the end? How could she not after seeing Superman and Lex side by side? It's the curse of Evil Overlord Lex Luthor to be done in by his Ladies. Didn't Lex learn anything from Miss Teschmacher?
Yes, there were way too many re-used bits from the first movie. Bryan Singer is a fanboy. He's a worse comic geek than I am. I think that he was so concerned with getting Superman right (and straight) that he went a bit overboard. That being said, DC Comics has been doing the same thing since 1938.
The child. I liked the addition of Jason. I've always liked the idea of a "next generation" of heroes. Stories where Lois finally managed to land Superman and raise a family were staples of DC Comics in the Silver Age. Most of them were imaginary tales. Some were tales of Supeman and Lois' doubles or of alternate Earths. And, of course, the slasher in me loves MPREG. Besides Jason was adorable and I liked the way he was played as fragile. As a hybrid that had to be carefully nurtured. That his survival was miraculous. And that he will someday grow into his father's powers but without his father's weakness to Kryptonite. That story could be amazing to tell if done well. Couldn't you imagine Tom Welling as Jason White someday taking on the name Kon-El? (So, it's not the clone story, but it could work.)
In the end, I just compartmentalized the movie as having occurred in an alternate universe and enjoyed the popcorn.
I recommend you do too and not stress over it.