You two are crying in the rain.
What characterization of Superman comes from that story, that still has a major impact on the character? For those of you that didn't graduate past the 6th grade here is the definition we are talking about when it comes to characterization.
char·ac·ter·i·za·tion [kar-ik-ter-uh-zey-shuhn, -truh-zey-] noun 3. the creation and convincing representation of fictitious characters.
In other words the personality traits of the character, or stated another way what makes Superman, Superman.
So what aspect of Superman's characterization in The Dark Knight Return continues to be an everlasting part of his character since? Their isn't any. He isn't a slave to the state.... in fact DC has tried making waves by making him "renounce his citizenship" of the US in the past. Granted that was more of a marketing ploy but never the less still a statement of fact.
Further your storyline example, "Superman going rogue and Batman stopping him." Isn't even universally true. They created an entire universe where Superman goes rogue, takes over the world, and does what he wants.
Hell they made a whole game out of it. In fact in that storyline ultimately the evil Superman is stopped by... well a good Superman.
And again a storyline is not a "characterization". Do you blame Miller for Martian Manhunter going rogue in JLA 88?
Because hero x going crazy is a pretty normal storyline, and has happened over multiple genres, and was not invented by Miller. The idea of "heroes fighting each other" also wasn't invented by Miller either. Furthermore even in Dark Knight Bruce only "wins" by faking a heart attack.
All you've shown me is that the Batman fans have a bigger market share in DC, and Warner Brothers correctly plays to that crowd because it is the larger market for them. In other words you two seem to have penis envy of the Batman fans because DC knows Batman is their highest marketing character, and play to that market. If that is your problem, your problem isn't with how Superman is being represented in The Dark Knight Returns, but instead how popular Bruce is compared to Clark.
If all you are is a consumer, (which I assume you are sense neither of you seemed to grasp the simple idea of "characterization") your only chance of changing the status quote is by growing the Superman fan base. You aren't going to do that by crying that Superman isn't DC's highest draw anymore.
Batman being more popular then Superman at the moment has nothing to do with how Clark's personality and characterization are presented after 1986. Because as I've stated those aspects of his characterization in that story only make sense in that setting, and has not been translated into the over all character. The Dark Knight Return did not have a long term change to how Clark is represented in the mainstream.
You want DC to start having Superman win these "fights" try growing Superman's share in DC Comic's profits. That is the only way it's going to change.