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.
But in a twist of Fridge Brilliance, if you beat him, you're basically like any given late game encounter in Nocturne anyway.
Argilla makes for one of the best healers in the game because her real self was a nurse.
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.
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?!