I would rather see Jax-Ur and Mala from STAS as the Kryptonian villians. It would be new character territory for the writers/director to explore.
Jax-Ur and Mala were just stand-ins for Zod and Ursa; there was literally nothing distinct about them (Mala was even voiced by Ursa's actress in her second appearance).
I liked all the casting in SR apart from Bosworth, who was just too young; Routh, Langela, Spacey (who could have been a fantastic Luthor if he hadn't been stuck playing "goddamn wacky Lex", as Paul Dini described it) all fit their roles. But if they ultimately decide to go in a different story continuity, they should probably recast, just for clarity. And for the love of god, nobody from Smallville