The trilogy, especially in its second book, Resurrection, takes a huge lot after Go Nagai's Shutendoji OVA.
Both stories feature an ancient prophecy related to a Stable Time Loop, which is created when heroes from the future who worked against their time plane's dark rule (Goki in Shutendoji and the Guardian in Resurrection) travel to the past and disseminate DNA in order to create lineages and secret societies that will fulfill the prophecy (the demon descendants and the Hunahpu, respectively).
The previous action ends up creating some of mankind's mythologies in the process, being respectively the Popol Vuh and many culture hero legends of mankind (Domain trilogy) and the legends about Shutendoji and other Japanese oni (Shutendoji).
The villains of both stories are also accidentally born of those lineages created by heroes. Shutendoji has the Demon Buddhists, evil sorcerers who have demonic blood, while Domain has Lilith, a Hunahpu who turns evil as a consequence of blood manipulations by the demon-worshipping sorcerer Rafelo family.
The main hero is a blond-haired young man with superhuman abilities who fights with a sword and whose name starts by J (Jiro in Shutendoji and Jake in Resurrection).
The hero's family is protected by two bodyguards, a big, strong dude and a smaller, more skilled one (Goki and Senki in Shutendoji, Salt and Pepper in Resurrection).
The villain is an older sorcerer of the same supehuman lineage (Kitani and Yonen Majari in Shutendoji, Alejandro Rafelo in Resurrection) that corrupts a female character into an evil seductress, who goes to fight the hero in the nude (Mrs. Tanemura and Lilith).
The hero travels forward in time in order to reach a dark, Hell-like world to save the soul of one of his parents, who has gone mad from despair there (mother in Shutendoji, father in Resurrection). He goes there from a futuristic spaceship from the future (the Alfard spaceship in the former, and the Balam and th Guardian space base in the latter).
The Hell in question is a reddish-colored Hell world populated by humanoid abominations. The hero travels here with a non-action female companion who acts as a load (Miyuki in the OVA, Dominique in the trilogy), and has to fight hordes of fiends. She then sexually harassed by the leader of the demons (the final oni in Shutendoji, Devlin in Resurrection), while the hero is seemingly killed by it, but comes back to save day with his liberated soul's inner light.
The final twist is the same in both stories, being that the Hell is a self-purgatory created by the negative feelings of its inhabitants.
In Shutendoji, Senki goes away to explore space with the demon race, while Manny does the same with the post-Hunahpu in Phobos.
Literature
The story contains also a metric crapton of references to Frank Herbert's Dune, another planetary epic related to bloodlines and religion.
Domain is moved by a brotherhood of people with psychic and genetic powers, the Guardian, similar to Dune's Bene Gesserit.
Blue eyes are associated to psychic powers in both franchises, in Dune because they come from the usage of Melange and in Domain because Hunahpu are born with them (or gain them later in life like Manny). In particular, the Nexus allows to give oneself Super-Speed, just as Miles Teg does does in Dune.
The protagonist of Dune, Paul Atreides, has twin children, Leto and Ghanima, which are born fully conscious and with psychic powers, just like Mick and his twin sons (although only Jake has those traits... at first).
The Tezcatlipoca snake is described as triple-jawed and is able to move underground, like the sandworms from Dune. The scene of Mick controlling it through the Balam dagger is similar to Paul doing the same with a worm.
Mick is forced to abandon his sons and depart to a messiah-like spiritual mission, just like Paul in Dune Messiah. Later, his son Jake goes in a search to find him, like Leto does for Paul in Children of Dune.
A hero is ordered to be trained in martial arts by his strict mother (Lady Jessica in Dune, Dominique in Resurrection). The theme of children being raised in a controlled environment with a specific mission is also recurrent in Dune.
Jacob is plagued with dreams about the future, like Paul and his son Leto, and some of them include his love interest. Egoism and their role as The Chosen One are also bitterly discussed. Another character in Domain, in this case Lilith in Phobos, has visions about humanity being destroyed and sets to avert it as a leader, like Paul in Dune Messiah.
As a child, Jake uses its powers to predict and avert an assassination plot, like the Dune siblings. Said plot is done is also performed by assassin expert in disguises sent by a technological corporation to kill the twin heroes (Solomon Adashek from Mabus Tech in Resurrection, Scytale from Bene Tleilax in Dune Messiah).
The twins are also opposed by a female genetic relative (Alia in Children of Dune - Lilith in Resurrection), who has been possessed by the memory of an evil ancestor coming to them through her psychic powers (Baron Harkonnen - Seven Macaw) - a result that is named Abomination (both stories). The influence of said ancestor turns her into a seductress who uses her body to ensure the loyalty of greedy men, the first of them being a corrupt priest (Javid - Quenton). In both stories, one of the twins fakes his death to deceive her, like Manny.
A female character with seductive powers is abandoned by her lover in a spaceship because she's evil (Lilith and Murbella). More similarities appear with Murbella's penchant for blashpemy, just like Lilith.
The usage of seduction for slavery used by Lilith echoes the style used by Bene Gesserit and Honored Matres in Dune. In an instance, it fails because a male target can also use it, being Manny against Lilith in Phobos and the Duncan Idaho ghola against Murbella in Heretics of Dune.
A scene in both stories portrays the twins trying a dangerous technique of their psychic powers when being left alone. They also use it to communicate with their father, or at least a memory of him.
In both stories, the son of one of the heroes mutates thanks to his immense powers and becomes an animal/human hybrid that acts as a ruler (in Dune, Leto, son of Paul; in Resurrection, Devlin, son of Jake). Said mutant ruler also submits his underlings by limiting a vital resource until leaving them in medieval level (the Melange in Dune, God's light in Resurrection).
The hero's son is warned about a dark-skinned seductress with enticing powers sent against him, but he falls for her anyways and this ends on his death. In Dune, it's Leto, son of Paul, for Hwi Noree; in Resurrection, Jake, son of Mick, for Lilith.
One of the heroes and his Evil Counterpart have a climactic blade fight, with the villain trying to gain the advantage with a poisoned blade (Paul vs. Feyd-Rautha in Dune, Jacob vs. Devlin in Resurrection).
People in the punkish future portrayed in Resurrection dye their skins, some of them in red, and take futuristic drugs. In the similarly decadent Giedi Prime from Dune, gladiators often have red-dyed skin due to the Elacca drug.
The sequence of Jacob and Dominique crossing the Xibalba desert is a direct reference to Paul and his mother Jessica doing the same in Dune. Even the design of the Twin Hero suits is a homage to Dune's stillsuits, which share a rebreather located over the nose and a contraption to drink water from it.
Another homage happens when the eccentric Merchant receives the POTUS to Lilith's mansion in the third book while smoking from a weed device, just like the ugly Honored Matre that receives Odrade to their hotel while administering some unknown drug.
A scene in the third book shows Devlin gaining the ability to somehow see through her mother's, the reversal of Paul at the end of Dune Messiah.
A character discovers special powers while being tortured: Miles Teg in Dune and Laura in Phobos.
A male character, displaced in time in some way, has to recover ancient memories of past lives to fulfill a mission and later undergoes a potentially lethal ritual to empower himself (Manny in Phobos, the Duncan Idaho ghola in Dune).
In the remote future, humanity becomes a space-faring civilization, as in the whole Dune universe.
The leads seek the help of secret organizations of natives (Sh'tol in Domain, the Fremen in Dune) and later a community of Jews (the Agler family in Resurrection, the Gammu group in Chapterhouse: Dune).
The sleeve weapons used by Salt and Pepper are similar to those used by Waff in Heretics of Dune.
The sequence in which the New Eden is discovered echoes the same with the abandoned alien cities in Philip Wylie's When Worlds Collide.
Another book by the same author, Gladiator, contains a main character with physical superpowers due to his father's influence who plays football with this advantage, like Manny in Resurrection. Mayan ruins of all things also appear there.
Myths and Religion
Although it is never mentioned in the story itself, "Mabus" is the word given by Nostradamus as the name of The Antichrist.
Lilith's son Devlin gains wings, a reference not only to the fallen angels, but also (possibly in-universe too) to the Babylonian Talmud where Lilith's offspring is described as winged children.
In the Kabbalistic text Midrash Abkir, Adam practises ascetism for many years after Abel's death until he is seduced by Lilith, who begets demonic offspring by him. The same happens to Jake in Resurrection after the "death" of the symbolic Abel (him). Like in the Abkir, the situation is solved by an older character wielding a special sword (Methuselah and Dominique respectively) and the demons are thrown to the abyss (although in this case Devlin throws himself).
In Phobos, Mick and Dominique take the form of an androgynous deity, like Adam and Eve do in another Kabbalistic book, the Treatise on the Left Emanation. The same work has Lilith begetting offspring by seducing Adam again.
