>Brainiac bottles the city/playable area, justifying limits to where you can go, because otherwise it would feel like bullshit when you can't fly around the whole earth You'd still have to make the player somewhat 'slow,' (as far as Superman goes) but just do some effects to make it feel fast, like Modern Sonic, and it can work. >Brainiac also put all the civilians (except for a few important NPCs who escaped) in stasis, but has let certain villains out to be the generals of his robot army or whatever.
And/or Luthor has figured out how to escape and recruited other villains as generals in his robot army, which fights Brainiac's, but they both fight you.