Superman also quite easily defeated Batman in Lex Luthor: Man of Steel.
And I agree that Superman vs. Batman is played out. It was interesting when it first happened, but now it's become incredibly derivative. Honestly, didn't we get enough "hero vs. hero" stories in the nineties?
One of the ugliest aspects of the said annoying fights in the 90s that you mention, is that fights are handled like popularity contests. Whoever is more popular wins. This is irksome because a fictional universe operates by the rules that it creates; you have to follow those rules in order for suspension of disbelief to work. And those rules don't take into account who happens to be more popular right now.
At the moment, the more popular of Superman and Batman happens to be Batman, and it leads many to forget the absolute implausibility of Batman defeating Superman. Heck, Superman, at least the one true Silver Age Superman, could probably beat the entire rest of the JLA (if it was for their own good, of course - maybe Kanjar Ro put them under hypnotic compulsion).
Putting aside for the moment the fact that Superman and Batman, being mature, intelligent adults, would not settle their differences via something as childish as combat, and putting aside that the both of them are smart enough to realize they are on the same side...putting that aside, and creating a theoretical situation where Batman and Superman are to fight, there's no way Batman would ever yield victory.
For the simple reason that Batman's main concept is that he is basically human. There is no weaponry in his repertoire that is either a) something that exists today, or b) is something that will plausibly exist very soon. In other words, he doesn't have a ray gun or a time machine.
Superman on the other hand...his concept is that he is superhuman, that he's "science fiction." If Batman is the X-Files, Superman is Star Wars. There may not be a Time Machine in the Fortress of Solitude, but it wouldn't be out of place there, either. Batman is the supreme expression of a human being in agility, intelligence, and strength; Superman on the other hand, supercedes human agility, intelligence and strength by multiple orders of magnitude simply because of his concept.
And the whole Kryptonite thing? Seriously, if all it took to beat Superman was just to have some handy Kryptonite on hand, Luthor or Brainiac would have
killed him by now.