The problem with most of that is that it exposes the technology to the world, and who can say if it will do more harm than good. And you know if Lex saw it he would try to recreate it. It's also a gross violation of people's rights. The government can in theory do much the same ... but they aren't allowed to ... and people don't want them to be able to. We could take DNA samples at birth and let them be used to solve criminal cases, but can you imagine the uproar if some politician actually tried to do it? Now imagine if the one doing it was a near all powerful alien from another world that no one had any way to stop? There would be panic in the streets, cats in trees, it would be chaos I say, chaos. For a lot of the rest of it, it's because of his moral compass. He could create a race of clones, but he probably thinks that he shouldn't. And while he could do whatever he wanted in a virtual environment, none of it would be real. As for the Kryptonite I'm never sure if that's a permanent thing or not. Smallville actually has one the best lines regarding Superman's struggle with not hurting people that I've heard. It's not just about not hurting criminals, but every time someone bumps into him, or every time they shake his hand he has to either give way or hold back. Imagine running done a hall and seeing someone and not being able to stop and the other guy being Superman and you bowl into him, but he's like a block of steel and just stands there not moving.
I never read the comics, just only the cartoons and live action movies. Superman is an alien and Batman is a vigilante. I say they're both the same level of tomfoolery. Both of them are increasing the difficulty level of crime. From heroes to villains to superheroes to super villains.