*Warning: If you haven’t watched it, this is going to be a spoiler.. 
i caught Superman Returns for the second time (like i said i would) at the IMAX theater a couple of weeks ago. I realized I missed several details of the movie the first time... I was kinda flying myself then.. Hehe.. surprise, surprise...
Here are a couple of common critiques from friends.
1. "Brandon Routh can never measure up to Christopher Reeve."
Brandon Routh was cast because he was deemed to be a brilliant superman. He was never meant to serve as a Christopher Reeve replacement. BR himself never let his respect for his predecessor take control of how he played the character. Instead, I think he managed to make this long-standing icon his own.

You might be confusing nostalgic memories with this judgment.
So get over this ridiculous CR comparison.
2. "Lack of romantic chemistry between Superman and Lois"
Superman was away for 5 years, and returned to find Lois with another man and a son.
Between them, were emotions of disappointment, regret, guilt, loneliness, anger, resentment, neglect…

PLUS given Superman's strong sense of morality, he knew he had to keep his distance upon realizing Lois had moved on.
3. "Superman's character lacked depth"
Superman I: Growing up, he had to learn how to deal with the responsibility of possessing his superpowers. He lived his teenage years, or rather, his entire life, as an outcast.
Superman II: as an adult, he was torn between trying to save the world and satisfying his emotional needs as a human being.
His entire existence was a lie. He made no real friends. The only people who knew his true identity were his Krypton and Earth parents. But really, how much practical advice could he get from them?
Jor-El to Superman:
You will travel far, my little Kal-El, but we will never leave you-even in the face of our deaths. You will make my strength your own. You will see my life through your eyes, as your life will be seen through mine. The son becomes the father. And the father, the son.

Apart from this "I'll always be here for you" speech, what else could Jor-El have said to prepare his son for life on earth?
Jonathan Kent to Clark Kent:
I know. You can do all these amazing things, and sometimes you think that you will burst wide open unless you can tell someone about it, don't you?... There's one thing I know for sure, son. And that is, YOU ARE HERE FOR A REASON. I don't know what it is, exactly, but I do know this much: it's NOT to score touchdowns.

And obviously, neither could his "earth dad".
It is no surprise Superman lived life essentially as a loner.
Superman to Jason:
You will be different, sometimes you'll feel like an outcast, but you'll never be alone. You will make my strength your own. You will see my life through your eyes, as your life will be seen through mine. The son becomes the father and the father becomes the son.

To me, this was more than a mere legacy.
In fact, I think Superman's speech transcended his father's.
This went beyond parental assurance, and rose to a promise of real support and understanding.
Superman led both lives to foresee the difficulties Jason might encounter.
One can expect Superman-Dad to furnish with more REAL answers when HIS son questions the meaning of his own existence.
The introduction of Jason White created new emotional depth into Superman's character. And since Superman/Clark could only go so far to form a real relationship with Lois, I think he relishes in the possibility that Jason could serve as a more comforting connection for him to earth and it's humanity.
So you said Superman lacked depth in this movie? I think he got deeper.
Just another thought:

It wasn't the first time that Lex Luthor's romantic interest found some moral awareness by the story's end. But even Lex developed a tinge of decency in this installment. I don't remember Lex holding any affection towards Otis (his sidekick in Superman II). There seemed to be a stronger bond between him and his help this time. His interaction with them was one of respect, not ridicule like before. And the main point in the movie that proved this was when the island collapsed and ended up killing the rest of his henchmen. Amidst the danger, Lex actually turned back and took a few grieving moments.
*can't wait for the sequel...