I think they did express them effectively, especially in the Ultimate Cut of the film. I just think that as a story, regardless of how one approaches it, is not exactly crowd pleasing stuff. It's cerebral and heavy.
Fair enough. I think that I would have taken a step back and said, basically, yes, we've identified something important here: Superman should not be an establishment figure, or an oppressive figure.
He's a decent, compassionate individual who happens to be powerful enough to challenge the establishment and make a difference in ways that most people cannot, or not as directly.
But then I would have moved further away from the source material and toward the idea that, while the methods are different, and their early experiences are very different, Superman and Batman have those two things in common: they want to make a difference, and they have the means to do so.
That moves the story away from the confrontation and toward a "World's Finest" type of team-up.
It's true that a team-up might have been more crowd-pleasing, but I think that it would also have avoided some other issues with the movie, as filmed, namely:
1) Batman moving in the direction of being an oppressive establishment figure (not good either, it's the opposite problem).
2) Adapting the Death of Superman immediately. It was just too early for that, in my view.
3) Reproducing the Dark Knight Returns confrontation so directly. It's true that the meaning is different, or at least potentially, but I think that simply doing something else would have been better. That fight simply doesn't have the same impact taken out of context, and I don't think that it really develops either character in a positive way.