Originally posted by ImpedimentManhattan couldn't create Kryptonite because he doesn't know what Kryptonite's chemical composition is. He'd have to have seen it before. Manhattan isn't omniscient, not even close.
Manhattan can control and manipulate matter. Superman, even with his demigod-like physiology enhanced by Earth's yellow sun, is matter. Manhattan can literally de-atomize Superman.Manhattan could also create Kyrptonite out of thin air, just like he made a glass castle out of Martian sand and created cold water and milk for Laurie to drink while flying around Mars.
Superman might be light speed/FTL and could potentially vaporize Manhattan, but Manhattan would just re-create himself and split into multiple bodies like did for his scientific research while banging Laurie in the bedroom.
Manhattan also has precog; He can see his own future. Unless Superman has some tachyons in his back pocket, then Manhattan will already have the advantage.