That old Wiseman telling you he'll stop a rampaging Id from getting to you, even getting called out on it by Id... totally unbelievable, right? Till you consider that he is Grahf and thus the same person with exact same powers.
Realizing that the entire human race in Xenogears is was artificially created by Deus may lead to questions or Acceptable Breaks from Reality regarding how a completely isolated culture retains the same language as the humans who were onboard the Eldridgenote Evidenced not only by the in-game text and opening move but also in reading the Eldridge's data and such. Then it comes to mind that Abel was the ship's only survivor, and could have spread these cultural aspects to the Xenogears planet.
On the other hand, Deus may have made humans speak in the language it was programmed in.
The odd part is that Solarians speak their own language, and if anything you'd expect Cain and the Gazel Ministry to be the ones that would use the language Deus was programmed in.
Maybe they do, Solaris's language is the original, flashbacks are translated for our benefit, and the surface language is something else.
Why does the super-gear Achtzehn have trouble fighting Chu-Chu, of all things? Because its main weapons are designed to jam gears' controls. Even when she grows to gear size, Chu-Chu is still an animal. She has no controls to disrupt.
While Grahf might sound crazy for his desire to end all human life and "return life to nothingness", humans are really just biological material meant to serve as the building blocks for Deus's new body. The instance Deus wakes up and their limiters are released, most of humanity will instantly die anyway and revert to nothing but biological building blocks. If people knew, most people would probably prefer Grahf to just quickly put them out of their misery, rather than allow them all to be swallowed up and melted down into Deus. If Grahf succeeds in killing every human, then Deus will have nothing to construct its new body and it would be relatively easy for Grahf to kill Deus after its birth. Grahf is just trying to fight against Deus in the only way he can, barring stealing Fei's body and using the Wave Existence to erase permanently Deus from existence.
The Gazel Ministry are the only major group that make up the Big Bad Ensemble who don't adjust their plans very much near the end of the game. They remain focused on reviving "God", and then joining with it, and the only major shake up is when they realize that the party are all compatible with the Anima Relics, and decide to use their bodies to escape being basically computers. Given that at this point the Gazel Ministry is basically just the remnant data of those surviving ones, that makes sense: their essentially programs/AI running on what limited coding makes up their "free will". They lose because they can't adjust or think outside the box anymore, hence why they never suspected Krelian would betray them.
During the scene in which everyone gets crucified on their gears, (and Chu-Chu dying for your sins), what even is the point, since everyone is sitting comfortably inside their cockpits or, in Maria's case, on top of Seibzehn. Probably justified in that the Omnigears' controls are mental, thus they require the pilot to synchronize with the machine. The crosses send artificial pain signal to the machine, which are then sent to the pilots through the mental communication channel, making them feel "illusionary" pain.
You can take Maria with you in a gear dungeon that is underwater. Presumably, every other gear's cockpits are waterproof, but Maria rides on top of Siebzehn. How does she not drown? There's the chance she enters the cockpit when the gear is underwater, rather than standing on top like most of the time.