Xenogears/WMG

We are bastards for killing Redrum. (spoilers!)
This is never touched on in the game, but there's so much evidence that I'm having a hard time believing it wasn't intended as Fridge Horror.

For starters, Redrum was innocent. All the murders that we attribute to him were in fact committed by Id, which means that killing him accomplished nothing. Not only that, but later on in the game you meet his kid. At first it just seems like a Pet the Dog moment, but let's analyze the backstory his son gives you.

He and his dad (ie, Redrum) were very close, until one day his dad vanished and never returned. This doesn't really add up, for a couple of reasons. For one, his kid looks like a perfectly normal little boy. And for another, he describes his father as friendly and kind, if a little bit scatterbrained... which doesn't exactly add up with the horrifying sewer monster who impales you on his claws and drinks your blood to heal himself. Curious.

Shortly thereafter, the plot reveals that Solaris has been kidnapping people off the surface and turning them into the Wels. One can infer that Redrum Was Once a Man, abducted and transformed into the creature he is when you meet him. (There's evidence of this: Bloody, the boss on the Wels ship, is a Redrum palette swap... and when you go to the labs where Wels are made in Solaris, one of the enemy encounters is Bloody Brothers - a pair of Redrum palette swaps.)

Redrum's son mentions that he and his dad always carried a matching pair of bells, so that even when they were apart, it would be like they were always together. Redrum had that bell when he was captured, and even through the procedures that turned him into a monster, he managed to hold onto this reminder of his son. It was probably the only thing that kept him sane.

When Solaris released him on the surface, Redrum knew he could never go back to his son - or, indeed, society - with the way he looks, so he fled to the deepest part of the Kislev sewers, where nobody ever ventures.

Along comes Fei's party, loudly broadcasting their intent to kill the "red monster" in the sewers. Note that the entire dungeon consists of chasing Redrum as he tries to run away and hide from you, and he never attacks you until you make him. How do you do this? By stealing his bell, the only thing he has left. That bell was probably the most important thing in his life, and you just up and took it because it was shiny. When he attacks you, he is furious. (Note how, when the scene changes to his POV, his breathing begins to sound angrier as it dawns on him that those assholes have stolen his bell.) He fully intends to kill you if it means getting his bell back, because he will not lose that last reminder of his humanity.

So, to recap: You stole a broken man's most treasured possession, murdered him pointlessly, believed yourself to be justified simply because he looks terrifying, and because he's That One Boss, you probably celebrated afterwards. You Bastard.

Humanity is alive and well elsewhere.
For whatever reason, humans decided not to visit the Xenogears planet after the Deus incident. Perhaps the planet was uncharted and far away from any settled system. Perhaps the final location of the Eldridge was unknown. Maybe humans knew fully well about the Deus incident and decided that it was a good riddance and did not want to touch the Xenogears planet with a 10-parsec pole. No matter the reason, it is exceedingly unlikely that every human was killed in the war that Deus was built for. Humans are still around, and had there been a Xenogears episode 6, we would have seen them.
 * Perhaps supported if we closely examine the opening anime scene. The Eldridge certainly looks like a colony ship, which would explain it being far out in space where no one else will just bump into it... There's also the chance that being a 'colony' ship might be a good cover up for 'get Deus the hell out of the populated areas of the cosmos'. Also, the bridge girls get a little more panicked when one mentions the 'main planet'. Not only does 'main' suggest that there are more then one inhabited planets, but that there's still something there that you don't want the super weapon going to visit.

Elly really is half-Lamb, but through her father, not her mother.
She thinks that Medena is not her biological mother, believing herself to be the child of Erich and her childhood nanny who came from the surface. It was also said that her nanny had a child prior to being sheltered by the Van Houtens who was 'lost'. At least in the English version, neither the age nor gender of the child were disclosed, so possibly this child could have been an adult son. It is possible that they somehow managed to recover this son and shelter him. This son had a relationship with Medena, and Elly was the result.

Both Medena and Erich were extremely evasive concerning Elly's beliefs; if it was untrue or if her suspicion was correct one would think they would have been more forthright, especially considering she was 18 at that time in the story. Also,  were quite interesting, insisting that Elly was not only the daughter of Medena, but himself, as if there was reason to doubt that too.
 * Elly has her distinctive appearance because . She doesn't know this at first, so she may suspect her parentage because of appearing different from her parents and other Solarians. It is entirely possible and very probable that Erich and Medena are her biological parents.
 * Original poster here--I prefer to believe that Elly's beliefs were unfounded, too, especially since two blondes can have redheads in real life. On the other hand, Sophia, for some reason, has a noticeably different hair color, which is especially strange as Xenogears had no problem reusing graphics, so   may not have much impact on her appearance... but at the same time,   are identical...
 * Jossed. The Perfect Works book explicitly states that the reason Elly looks different from her biological parents is because she's a reincarnation.

The entire game is Shinji Ikari creating a world where he's a Badass Kung Fu Master instead of a spineless wimp.
Elly is a mix of Rei's selfless and sacrificing personality and Asuka's physical body.

Deus is a stand-in for Adam/Lilith.

Solaris is a metaphor for SEELE.

Grahf/Wiseman is Shinji's Father if he had his personality split into two. That Lacan is also Fei is icing on the cake!

Fei hates gears not because they cause war, but believes his martial arts skills are superior.
This could be coming from his subconscious counterpart, Id, in combination with his Superego's stance. He already has the power to destroy even Gears with a single punch, so it would be a little insulting to his self-esteem.

Id gains his armor and clothing from the Zohar.
Id, in his true form, could be an energy being overlaying over Fei's image, and have the illusion come from the Zohar the same as AWGS has a power supply sent through energy waves.