They could also have supes start early in his career so his powers have not developed too powerful yet, this could mean that streamlined gameplay like in Batman: AA, while regular supes would just punch through any door unlike bats, a young clark could have to take the sneaky or long route and still make sense. They could use Christopher Kent(Nightwing) or Conner Kent. Chris is not as powerful or as invulnerable as other kryptonians (he was born in Phantom Zone, he is the son of General Zod and Ursa, kryptonians, adopted by Superman/Clark)
Also Chris's backstory and costume are cool and would fit if they decided to include a part where you say team-up with Red Robin, DIck Grayson or Bats? Maybe include enemies from batmans backstory such as Joker, Freeze, Ivy(maybe she could control him with a pheromone, sending him to kill bats, you coud play as Bats trying to free him and restrain him, or play as supes trying fight against the control with*sigh*timed button presses,if you miss Bats gets ripped to shreds or disintegrated)
They could also use detective mode (using the multiple types of visions clark is endowed with (using his knowledge of lead he could find hidden kryptonite/magic based traps.) They could use the multiple flavours of Kryptonite beyond green such as red which takes Clarks morals, inhibitions and ambitions away making him ruthless and selfish for some scenes, maybe some scenes as clark? Include smallville? A section of the game could take place in smallville? Hero cameos? (Batman/wonderman/Supergirl etc.)
Silver K makes him lose his mind, maybe including a part of the game where he goes nuts? (scarecrow could make a fear gas utilizing different K's) similar to Arkham. Maybe a phantom zone part where clark is vastly weakened and must use sneaking, wits and his natural strength gained from farming with his parents. Maybe a love interest to boost character development? Lois or Lana (Thara if they used Christopher Kent (Nightwing)
Make it less about abilities and his feats and more about his character, his views his humanity, maybe some moral dilemmas. Have his character tested, perhaps Lois/Lana/Kara/Parents are killed by one of his enemies and he is tested on his rule of never killing? Seeing him beat someone to a pulp and struggling to hold back like his usal self would be cool. maybe an end fight against his bigger enemies (Brainiac/Lex Powesuit/kryptonite tonic steroid/ Dark Sied)
Like Arkham Asylum which took place over the course of a single night in Arkham they could say have a bomb threat made by a group of Villains, the bombs have been placed in various sections of the city, they are using it as a distraction for a larger scale threat but you must primarily find villains (probably guarding a bomb, some investigative parts as Clark Kent? Utilize multiple visions and super hearing ect. (the injustice league/ include an alternate dimension JLA(villains?) Maybe a space section? Maybe the game would not even actually NEED free-roam as that would use up resources that could be used on graphics or other gameplay mechanics which were prominent in Arkham.