Say a new kryptonian one that was more of an average joe showed up on or was revealed to have been on earth for years and nobody knew it because he was living as a homeless person and when he started making his move he was initially helping people and doing what Superman was doing all the while coming off as more modest and slowly gaining the favor of the population using his superior intellect to heal the sick and dying. Eventually becoming more of a savior to the human race than even Superman to the point that he has everyone drinking his cool aid and has nations freely surrendering to him and submitting to his rule (which is really more of a form of government that removes class and keeps all humans under his thumb) and even turns the earth against Superman.
And in their confrontation this kryptonian says to Superman
"Do you know what your problem is Superman? You don't know what it's like to be down in the dirt to have nothing. You grew up on a farm raised in a nice quaint little town and when you got your powers you just decided to be a freaking hero but back on our home planet I wasn't any different than I am now I wasn't the most handsome or the most talented I suppose that's why my theories and ideas where often shoved aside or dismissed by the scientific community point is I know what it's like to have to build something from the ground up. Do you know how many humans die from disease because they don't have healthcare or how many children go missing leaving their parents broken? I do because I have actually lived amongst the humans I wasn't living on a nice little farm like you I've seen their pain their anguish I've seen them pray for a miracle I've seen them look up at the sky and ask God or even you why? Well guess what you don't hear them because you don't see these people as important you just punch bad guys in face and screw Lois Lane! You don't even know their names but I do! Thanks to me their will be no more disease and no more missing children I've done more for humanity in a few months then you have in years! So what if all I ask is for them to accept my guidance what has free will gotten humanity so far? I may not be the best but I'm the best chance humanity has before it drives itself into self destruction."
What would Superman say to such a villain and how would he handle him? Especially if this man was actually doing good for humanity him being removed would undo all that good despite him having committed crimes. I should also point out that this villain has a device that makes using the Phantom Zone impossible.