Superman is a double-edged sword, no matter how you look at him. One edge, he is kind, uses his strength to save the innocent civilians and does as little damage to the city as possible when he has very large fights. On the other edge, Superman is overpowered, his storyline has been booted and rebooted to the point where a "true canon" is nearly non-existant, and he is just a very hard character to write for. No matter how you look at it, being the first superhero comic book ever made Superman the equivalent to unmolded clay. He didn't even fly at first, he just jumped long distances. It was a later comic book writer who finally just said that he could fly. Then he got every single power known to man. He is powered by the yellow sun, almost completely indestructible, with super speed, super strength, X-ray vision and laser eyes. Some of his powers were brought from even more obscure places, like being able to hear from across the entire world, materializing brick from his "Brick Vision" on top of having a photographic memory, the ability to slow his pulse to make it look like he was dead while he healed and the list goes on and on and on.
From a writer's standpoint, Superman was a ticking timebomb. It is nearly impossible to stay loyal to such a wide and expanding source material when not even the original company can't seem to get such a laundry list of powers right. It got to the point where they were pulling any power out of thin air in order to give Superman the edge, then his powers get rebooted and he either gains a new power or loses one of his powers he once had.
With all of that in mind, try thinking up game mechanics around such a broad spectrum. Think about what would be considered thugs that could bring him down. The NES Superman game made him vulnerable to bullets. Maybe they were kryptonite bullets? There really needed to be some nonsensicle terms in order to get Superman on board without him flying into space and laserbeaming his opponent from orbit. Here was a superhero that can literally take down armies within seconds and you are now tasked to make a game that would be considered challenging with such a character.
Superman for the Nintendo 64 came up with the very stupid idea of having Superman sent into a virtual world that looked like Metropolis (?) and the air is filled with kryptonite so you can't... do... powers.... Look, no one bought it when they devs said it. The real problem with this whole scenario is that Superman for the 64 is considered the worst game on the system, but there is a game of similar quality for the XBox/PS2, Superman Shadow of Apokolips.
You fight robots but you can't use any attacks except for the attacks that hurt certain minions. They can't be bothered to come up with any reason to explain why Superman can't scrap this entire army of bots, it just gives you the jankiest controls with which to make the attempt. This game is a meaningless waste of time with the worst game mechanics and 3D cut scenes known to the Playstation 2. It really seems like one of the worst problems with Superman games is his flight. Where Nights Into Dreams and Mario 64 who seemed to get the flying mechanics down to a science years before, Superman games just can't seem to get them right.
While there haven't been any stand-alone Superman games to reach critical or commercial success, the Justice League games involving him usually turn out pretty decent. Nether Realm Studio's Injustice games actually use him to much more of his potential. They just come up with the plot device of people taking super pills and being able to actually hurt him with their bare fists. Yes, this is the lengths they need to go to to sidestep that little problem of him being able to liquify them with a backhand.
What needs to be done to create a Superman game that actually works, obviously there needs to be a good story, but there also needs to be an enemy that can hurt him while also being able to keep up with his speed and universally overpowered strength. Pulling off such dangerous opponents would be very tricky to write around without getting too violent. The whole idea is not to nerf Superman's powers to an inconsiderate rate. Using his powers that make sense while also having the power to demolish entire structures with a punch is what every Superman fan has dreamed about. Giving him short distant super speed and ice breath would also be a great bonus in this mechanic.
Bringing on Doomsday as a final opponent, or even Darkseid would be preferable after a long storyline, using them as a climax. Batman v Superman the movie could have worked as a video game if you added in some more main line DC villains. Brainiac has been a little over used as of late, but he could also be executed brilliantly in terms for a Superman adventure game. Without a very deep understanding of video games or a deeper understanding of the comic book super hero character, you're not going to go far with the fans. Mixing and matching storylines for a video game is acceptable, so long as you keep it fun.
That's the key detail, whether the game is fun or not. If we don't feel like Superman, then the game takes a terrible hit. Perfecting Superman's power level in comparison to the villains is paramount but perfecting his character is equally as important. It's these huge, mounting details that befuddles video game developers to no end. This would require an entire team with a solid gameplan and a considerable budget to accomplish. It's this reason that makes it seem like you just can't get Superman right in a game while Batman has ever growing potential, given his brilliant and strong mortal status. It's Superman's own power that destroys him, ultimately, and the free wielding way comic book writers treated him like a literal god in terms of his infinite number of powers. Come up with a solid formula for him and you might be able to release something that will surprise everyone who said it couldn't happen. Until then, he still has an awesome animated series and a good number of comic book storylines. There's a ton of things that make Superman great already, I guess video games are just too magical a concept.