Shin Megami Tensei: God is Evil
Japan has had a reputation of making video games that involved fighting against enemies that possessed divine powers. Some of these games used divine powers that were based on actual religions. One example, the religion of Christianity. As detailed in the article Shin Megami Tensei: a Game of Consequences the player played a game where the main character gained the power to summon beings to fight in a Tokyo that was being besieged by monsters. Monsters, that Shin Megami Tensei revealed, were based on the mythology and theology of today's world. And while Lucifer does make an appearance, he does not affect the plot in a major fashion. Of course, the sequel to the original Shin Megami Tensei game changed things up a bit. Published in 1994, Shin Megami Tensei II presented the aftermath following the original game. Long story short, the forces of Heaven and Hell were poised to have their forces battle it out for the dominion of Earth, and the main character of this game gets the chance to choose which side he supports, or shun both sides. But Shin Megami Tensei II did things differently by including the plot twist that the main character was an artificially-made human that was supposed to serve as a Messiah for the Messians who worshipped the Christian God. The second plot twist was that the Messian God was YHVH, or Yehowah. Also known as the Christian God. And in Shin Megami Tensei II, YHVH was so bad that everyone wanted to see him destroyed. And while this may seem like a blasphemous portrayal of God, it is. But since Japan was a nation where Christianity was not a major religion, game developers like Atlus could acknowledge some questionable aspects about Christianity without much protest. Such as the belief that Yehowah was some infallible being, but was recorded to have condoned the ransacking of entire villages, forced a (failed) paternal homicide, and drowned an entire planet of people because the majority oh humans were not completely subservient to him.
Shin Megami Tensei II
As stated before, Shin Megami Tensei II was a game made in Japan. As such, there was most likely not as much protest when it came to using Christian theology as a source to create a game where the player kills a divine being. Of course, the game gives some justification as to why beating down YHVH was needed. See, YHVH was portrayed as a supremely powerful being who desired to not only rule the physical world, but the divine world as well. To do that, YHVH basically imprisoned or tortured divine beings from foreign religions or beings who did not fully agree with his doctrine. This, of course, created Hell. And even amongst his followers, YHVH was regarded as somewhat too extreme. This created one of many plot twists by revealing that the player character of this game was an artificially created human meant to be used by some Archangels to help spread their Law and Order throughout the land. Once YHVH learns of this plot, he not only condemns his old allies, he even threatens to commit genocide upon the Earth itself. And since Shin Megami Tensei II was the conclusion of the original Shin Megami Tensei game, the world was already ruined because of nuclear weapons. Now, while YHVH was irredeemably evil in this game, Atlus, the developers of Shin Megami Tensei II, provided one reasonable explanation. The world of the main Shin Megami Tensei universe was very corrupt, and something was affecting YHVH in an incredibly negative manner, like an illness, which made him act the way he does. Unfortunately, due to an increase in overseas popularity, that reason was never presented.
As a result to the Shin Megami Tensei franchise gaining popularity in Western countries, the idea of God as a villainous force was lessened. While saying Yehowah being afflicted with might have made him somewhat of a sympathetic character, Atlus decided to get rid of idea for its later games. Like the spin-offs. Where a prominent Christian figure that was close to God could be portrayed as being full of themselves. Which implied that God himself was alright, but those who follow him tended to exhibit extremist viewpoints. For example, in the 2011 game Shin Megami Tensei: Devil Survivor Overclocked, the main source of conflict in the game was that a significant portion of Tokyo was forced into a lockdown enforced by the Japanese government. For this franchise, the reason why parts of Tokyo were closed-off was predictable. Somebody developed a method to summon demons through a digital program, said method was spread amid a huge cult, and pretty soon this same technology started to spread into the civilian population. And then the widespread murders occurred. Through some side-quests the player eventually finds out that Christian divinity forced the Japanese government to enforce Japan's lockdown. Which makes sense to prevent a potentially murderous person from escaping into the wider world.
Like other Shin Megami Tensei games, siding with a force of Chaos is an option. Shin Megami Tensei: Devil Survivor Overclocked makes the forces of Chaos somewhat justifiable. The representative of Chaos, Naoya, turned out to be Cain from biblical lore. Basically Cain's punishment for murdering Abel was to endlessly reincarnate into a new human, but with all of his memories, including his murder of Abel, completely intact. Understandably, being forced to reincarnate with the memory of murdering someone in your first life left Naoya angry against God. So much so that one of the endings of Shin Megami Tensei: Devil Survivor Overclocked involved following Naoya's advice when it came to destroying the lockdown, which basically meant you becoming an Overlord with absolute control over all of the demons in Tokyo. Unfortunately, a playable epilogue showed that following the directions of someone who really wanted to hurt God meant that Heaven would take offense and send someone to stop any act of rebellion. Like Metatron, the angelic vessel of God who served as his voice. However, depending on how you treat those who seek to harm you, the new Overlord (you) may gain rising support in your eventual showdown with Metatron. Mostly by pointing out that while Metatron and the forces of Heaven would sacrifice mankind for the greater good, the main character as Overlord was going to fight God and all of his followers to spare all humans from his wrath.
In the newest game Shin Megami Tensei IV: Final the character that players control gains new abilities to fit his new, supernatural job. God-killer. Which basically meant that the player had the ability to slay the actual deities of foreign religions permanently. Like YHVH, who makes a prominent return to the Shin Megami Tensei franchise. But at the very least Atlus gave a new explanation that would make beating YHVH plausible to Western players. He was not the actual God of Christian theology. Just an avatar of The Great Will, a legitimately benevolent entity. In fact, The Great Will actually supports you in trying to destroy YHVH. But, Shin Megami Tensei IV: Final does try to make the player sympathize with YHVH by saying that since YHVH made himself the supreme God in a monotheistic religion, the loneliness of the sole entity with his level of power drove him mad. Of course, seeing as how most games made it so that YHVH was seen as an overpowered tyrant who would destroy humankind on a whim, sympathies can be lowered.
God in the Shin Megami Tensei franchise has always been portrayed as a divine jerk to humans. But since this franchise was made in a country that may see the widespread worship of this sole entity and all of the wars, destruction, and other questionable actions done in his name as baffling, it makes some sense. Especially for people who were members of more polytheistic religions.