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.
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.