As I've said, in my head this is largely just Skyrim: Metropolis Edition.
Big open world to explore, lots of stuff to distract you from the main story. I want something I can burn a thousand hours on and still want to return to.
I'd maybe use Maxima as the main villain; she's shown up to woe Superman and add earth to the Almerac empire. I know everyone always wants Brainiac but Max is a fun, unexpected twist that makes for a different kind of story than people are used to from Clark. I'd lean hard on the "space Rome" aesthetic and avoid the....less appropriate....bits of Maxima's reputation. She wants to add Kryptonian strength to the royal line; she's a badass queen who takes what she wants and what's best for Almerac, not some bratty space slut. Not really dedicated to using her, but I wouldn't want to do somebody expected like Brainiac, Lex, Zod, or Darkseid. Not as the main villain, I think they could be in the game in some fashion, but perhaps the main story shouldn't be something so....predictable. If not Maxima, then at least not one of the obvious choices either.
Reputation meter like Fable that swings between Golden Age Outlaw and Silver Age Nice Guy, which would impact the story in various ways. That ties into what I was saying about "threats" and "challenges" too; it's not "city as a health bar" but if you're trying to be the Nice Guy, you probably shouldn't throw a bus at a bank robber.
Skill trees akin to Elder Scrolls so you can build your own kind of Superman and focus on different skills and powers. Including non-combat stuff, maybe even a skill tree for the crazy/weird powers (one branch for solar flare type attacks, one for zany Silver Age stuff, one for 90's electric/energy?), combat skills (a branch for boxing/MMA, a branch for Torcasm Vo?), maybe a skill tree for Clark's resources (a branch for Fortress tech, like Zone projectors, a branch for earthly resources like calling in Steel or SCU?).
Faction groups you can work with and rise through the ranks. I figure some groups are dependent on your rep; like STAR Labs wouldn't work with an Outlaw but Cadmus would, and each would offer different missions, rewards, stories, and vendors.