It's not like "The Man Of Steel" or any future Superman film cannot introduce who Brainiac is and explain him. Superman isn't indestructable. He's invulnerable, but he can be hurt. Watch Superman II and you can see Superman in pain during the Metropolis showdown. First when you see him shake his head from being attacked by Zod in the Donner Cut and Non in the Lester Cut. Then after he hits Non up through the street, Clark's wincing and testing out his right hand from the fact that he hit Non so hard. Not to mention that it hurt when Zod punched him in the gut so soon after Ursa threw the manhole cover at him. Besides, there's many ways to do Kryptonite and non Kryptonite foes. Not all of them have to be Doomsday.