Regarding the Bonus BossDemi-Fiend: he's immune to all attack types, except for gun, earth, and almighty. Almighty can't be blocked by anything, anyway, but gun and earth can be explained if you remember that in Nocturne, the strongest Magatama shields you from all attack types... but gun and earth attacks aren't avaible in that game.
Fridge Logic kinda kicks in from a canonical perspective when the Demi-Fiend could potentially nullify Dante's gunshots in Nocturne. Though it could just be because the developers didn't think to create a separate type of attack in that game, if you're looking at it from the gameplay mechanics.
in DMC canon it's stated that Dante makes his bullets via magic so there's some justification.
Why does the Demi-Fiendkick your ass so hard? Because he's the protagonist of one of the most punishing games in the series. Makes sense that having him beat up a variety of ragequit-inducing bosses makes him one of the most devastating fighters in the entire series.
Argilla makes for one of the best healers in the game because her real self was a nurse.
Similarly, Heat O'Brien, the Guest-Star Party Member has more healing skills than any other type of skill, despite being the real self of the Embryon's musclenote He has one magic attack skill, two physical attack skills, two physical boost skills, and three healing skills . From a Doylist perspective, it's because he has to carry Serph though the fight, but from a Watsonian perspective, it's because he was a doctor.
Cells are so valuable in the first game for the Temple because they are Karma technology intended to study the Junkyard's data.
For some it can be seen as weird how Embryon, Sera, and Angel are reincarnated as younger versions of themselves with more normal hair colours. Remember that data can also be recycled as well as deleted!
When you fight the Angels, Uriel and Michael lament on why God is not answering them. Then you realize that the game is based on Hindu mythology and that the god that they were trying to talk to is not the god that they think it is.
Serph from Junkyard is nothing like the real Serph. Data Serph's lack of personality reflects Sera's lack of understanding of who Serph really was.
Why do so many Bonus Bosses from the second game reference Shin Megami Tensei II? Both games have you defeat that world's Top God as the Final Boss.
While it does make sense that a beach is a part of Sera's virtual paradise to begin with, it makes even more sense when you know that Cielo was her friend. Cielo is from Jamaica, which is known for its beaches.
Why do Hunt skills ignore immunities, repels, drains, and resistances? Everything in the game can be eaten! If it's not edible, you can't gain AP.
Beelzebub and his guards are sealed behind a red wall in the first game, so why didn't those guards die of starvation by the time Serph and co reach them? Some of the Mooks outside claim that a seemingly infinite number of rookies seem to spawn from the base, and more appear no matter how many they devour. Given that the whole Junkyard is a computer program, there might just be a spawn area.
Both Harley and Mick the Slug are both cowards, but why did Mick manage to stay calm when Harley completely lost his head? Judging by the ex-Vanguard who says that Beelzebub had guards before the Red Wall sealed them off, and the fact that that wall will be there on the first visit, the Embryon visited the Vanguards shortly after Beelzebub went berserk. Harley's had a really bad day before the Embryon even showed up on his doorstep; the other monsters who ate his men are just the icing on the cake after one of his own men ate his subordinates.
Gale's Atma is named Twister. Angel's is named Maelstrom. Both are vortexes in the air and water respectively, hinting at their link as former lovers.
Cielo is weak to ailments. It's implied that the original Cielo went insane and died before experimentation. He's weak to poison because he was drugged, mind ailments because he went insane, etc.
In the second game, the Karma Society soldiers have sealed away Indrajit/Meganada in a sort of stasis. It turns out to be one of the first people to have the Atma Virus tested upon. When were they sealed, what's to say they're not unconscious, and how hungry must they be?!