Why is Atsuro your strongest physical fighter initially, even though he's a scrawny hacker? He hacked his COMP!
Why does Belial say at the end of Day 6 that humans are more qualified for the throne of Bel than demons? Because humans invented something that can allow humanity to go toe-to-toe with demons.
Why do God and his Angels abandon the earth on Yuzu's 8th Day? Because as Lucifer said only he will never abandon us.
Why does Naoya suffer from Redemption Demotion in Atsuro's route? Because he simply can't be arsed to fight Babel for you. Why should he exert himself for a cause he's not particularly invested in?
Lucifer, I read your book! Up to this point, his motivations have generally be described as For the Evulz and It Amused Me, but look closely at what Nebiros and Belzaboul (on Naoya's route, at least) say upon their defeat—both of them say something to the effect of "my master will be pleased." Combining that, on either Gin or Atsuro's route, Loki will imply that Lucifer will visit the human realm, despite his apparent lack of interest of the title of Bel. And finally, on Naoya's route (at least), Belberith hints at wanting to overthrow Lucifer once he becomes King of Bel. While this may seem like a stretch, it seems that Abel's involvement in the conflict was planned by Lucifer, especially if what he says about being the main character's father are true: Worst case scenario, it'll at least be fun to watch. However, if Abel wins the throne, he had someone that got rid of a potential usurper. Bonus points if he decides to rebel against God (anyone else remember Nocturne's True Demon Ending?). And hey, even if Abel decides to be a lapdog of God's, all Lucier needs to do is wait for him to screw up. He stands to gain something regardless of the outcome.
The MC is a reincarnation of Abel. In other words he's a Bel.
The two worst endings, the Early Bad Ending and Yuzu's, are perfectly typical SMT Law and Chaos endings. In the Early Bad Ending, you escape the lockdown on day 6, causing the angels to kill everyone in the lockdown and remove free will. In Yuzu's ending, you escape the lockdown on day 7, causing demons and demon tamers to escape the lockdown and resulting in the world becoming a Social Darwinist anarchy. However, these are accidental outcomes of your own stupidity, not your intentions.
God's Ordeal is apparently rigged. If you become King of Bel, then either humanity (represented by the MC, since this is a morality play) fails by accepting God's control, or fails by the rebelling against God (at which point God plans to take over regardless). But that's kind of the point: humanity can only remain free of God if they Screw Destiny and Take a Third Option, proving that they have the wisdom to use their power responsibly.
In a meta-example, the series is a Deconstruction of what would happen if STEVEN has succeeded in sending out Demon Summoning Programs in Shin Megami Tensei I. In that game, everything get cut short when Thor nukes Tokyo.
Why does Black Frost only follow you in two routes? Well if you take Naoya/Kaido's Route you are embracing your role as King of Bel and he is a demon so he obeys you as his lord and you have proven to share his philosophy. Why does he follow you on Gin's Route even when you want to banish demons? Because you are working to protecting all of the humans of the world from demons. Thus he'll be willing to send all demons including him home to protect the weak. However Atsuro's route plan despite allowing for peaceful coexisting doesn't. Because it would enslave all demons - worse still it oppresses the weak demons and doesn't even protect humans given they can still use them against other humans. Just fleeing wouldn't interest him in Yuzu's route and not only would he not be interested in serving God he wouldn't have him anyway!
When you first revisit Keisuke about 2 hours after he leaves your party, you'll notice that he's gained some experience and new skills, including some most likely cracked from human adversaries. And it turns out that given his later behavior, it's very likely he gained these by killing some people. So when Atsuro tells you not to let Keisuke become a murderer, you're probably already too late...
More a meta-example rather than in-game. Let's just say you're a newly-wed couple. Then you finally have a child. Turns out the child is a reincarnated killer with all the memories of four thousand years living in the world INTACT. Granted, you won't even know who exactly the child is, but seeing that he's more likely to be anti-socialyet earning perfect scores in every test would be, well, unsettling...
Speaking of which, Naoya spent most of his "childhood" being raised with the protagonist after his parents died. Considering how focused he is on his "brother," it makes you wonder whether he had anything to do with that...
