A small example, but the Batter's add-ons resemble the circular training weights used on baseball bats.
The name of Japhet's battle theme is a reference to Lost in Translation, which is about a famous actor who goes to Japan to film a commercial and ends up feeling highly alienated in the process. This could mirror how Japhet planned to please the Elsens and ended up going mad from his failure.
The game consists of The Batter completing three zones and then going to The Room, which is treated as returning to past events and serves as a sort of "home" for The Batter. Scoring a run in baseball means advancing around three bases and returning to home plate
There's a reason why the Elsens in Zone 2 are so afraid of everything: The Elsen can't reproduce, so it follows that they'd be extra careful about threats since their numbers are limited.
As Bad Batter's form is meant to not be a literal transformation, but instead to represent how the player would perceive the Batter upon opposing him, the Batter might not look exactly the same to everyone, hence all the interpretations of his eyes.
Which would also explain why the Elsen were so easily fooled by his tie.
Choosing the Ashley Bat over the Aries Card is not only Awesome but Impractical, it basically ensures you're doing all you can to murder your wife and creator.
In Zone 2's library, there's a book called "The Toad King", referring to a masked man who defeats a toad. This could be a reference to Zacharie, the mask he wears when we meet him resembling a toad. It becomes mild Fridge Horror when you realize he gains the cat mask after Valerie's death...
Mortis Ghost has stated that the cat mask was not made from Valerie's face.
If you think about it, by killing Dedan alone and purifying his Zone, you have doomed the entire world - all elements necessary for life were manufactured there.
Then, there's the sole Elsen left living by the end of the game. While it seems unlikely that he'll become a Burnt due to being calm and will survive the demonic dolls - assuming if they want to attack him - he'll eventually die from lack of smoke or food.
The fight against the Critic Burnt is far more terrifying when you realize his head still resembles an Elsen's— implying that he might not have become fully Burnt when you fought him.
Zone 3's purpose is to produce sugar and export it to the other zones, so life for them is bearable. Except... by the time you've gotten to Zone 3, the other two zones are already gone and the Elsen in Zone 3 are either just going to end up dying and being turned into sugar anyway, or are addicted to sugar beyond the point of ever recovering meaning that the entire factory of Vesper is now essentially a functionless and pointless economy that creates death simply to fuel those who are creating death, all just filling up the fortress that keeps Enoch safe from the spectres. Yeah.
In Zone 2 you can meet an Elsen who is freaking out because somebody locked him out of a safe house. Later, after purifying Zone 2, you come back to the safe house and unlock it to get one of the objects needed to get either the Ashley Bat or the Aries Card, finding the last Elsen in the game (who was also the one who locked himself inside the safe house during the timed mission). Doesn't seem that bad until you realize the reason he was safe is because he locked himself in there, and assuming the Secretaries can't go through solid objects he could have stayed in the safe house until the Judge came to Zone 2 (if you picked the Special ending). So, to sum up, you broke into a bunker, stole everything you could from it, left the door unlocked, and left the last Elsen in the universe at the mercy of the Secretaries right outside his door. "Oops" doesn't even begin to describe it.