The solution for a Superman game to work is to have you play as a young Clark Kent who just moved to Metropolis and is still learning and growing his powers. Metropolis should be huge and act as your main hub to do activities and side missions. Main story missions can occur in other places Warworld, Atlantis, Brainiacs ship, or wherever, but you always return to Metropolis between them. By the end of the game you should be able to zip and fly at breakneck speeds and be powerful as fuck, but at least there will be a progression up to that point and you'll have to earn your way to it.
Batman has had plenty of games, and Wonder Woman is getting her first big game too. There's ways around Superman's powers and soon they'll be running out of excuses as to why we still don't have a AAA Superman game.