Eh, Post Crisis rules: Kryptonians can hold their breath for a long time, plus the idea that a Kryptonian's atmosphere is somehow less dense in oxygen might be born out in MOS, considering that Clark is exposed to it for a long time before it actually effects him, and he recovers consiousness and stabilizes quickly. And I've got a pet theory that the atmosphere's composition is what triggers the gravity warping flight ability: only Zod and Superman fly, while Faora hovers between shots in the plane, and all three of them were exposed to the atmosphere without helmets able to activate.
My main thing with kryptonite is I want a limited, finite and short supply. Make that chunk Luthor has all the kryptonite in the solar system, and suddenly it becomes a resource. Don't make it something Earth science can synthesize; that opens way too many plot holes about why Luthor can't quickly kill Superman. I also prefer the idea that the World Engine either contains it as a power source or creates kryptonite, and that the process is so complicated and energy reliant that even other interstellar foes like Brainiac and Darkseid can't quite replicate it without doing something on par with terraforming a planet. Makes it special and much cooler than a generic Achilles heel plot device.
My number one goal would be to forever cast out any kind of kryptonite situation where it become a lazy man's plot developer, like in the Silver Age or in Smallville.