Or even without a story element to strip them, start the game in present-day Metropolis but have the main chunk of the game be a sort of flashback leading up to the last couple hours or so. Start with a teenage Clark adjusting to his powers and not knowing what they all are, dealing with disasters in and around Smallville, moving to other spots around the world as he learns more of his ability, Fortress of Solitude as a sort of main hub, etc.
Eh, I don't know. I'd prefer everything to stay set in Metropolis.