Luke as Peter Pan and Robots as Fairies
So first we will start with the obvious, which is Peter Pan himself. In various sources, he is a young boy of either fairy or human origin, abandoned by a human mother or run away from his nursery or raised by fairies or something similar. In Ghost Soup, we have a clear equivalent in Luke. Orphaned in the Sector Delta Niner War for Independence, Luke was taken to the first robotic orphanage on Sirius Beta. For the continuance of this metaphor, robots of Ghost Soup are stand-ins for fairies in Peter Pan, as will be elaborated upon later.
So Luke is taken in by these robots, where he has a collective behavioral example, rather than an emotional connection with a maternal or paternal figure. Except he does have an example of the ideal paternal figure, in the images of great Fleet Generals pasted upon the walls, as seen in his flashbacks to the orphanage. These men are everything a hero should be, but nothing a decent father should be, thus giving the orphans a considerably odd outlook of grownups.
Furthermore, the robots, with their different culture and laws, are like mystical fairies in a way, particularly to a child. There is something about a being that is not alive, is not emotional, and yet that looks like a normal human. This detached kind of parenting is actually seen in breeding farms currently, when animals are raised by machines and do not receive the social and societal interaction as infants that they need to grow properly. Imminent fast-food death notwithstanding, this is very similar to the robot nannies and orphanage bots of Ghost Soup.
Raised without adult human contact, Luke, as our Peter Pan, runs away at the age of 12 and enlists as a cabin boy on a freighter. Thus he is now truly a lost child, surrounded now by more adult humans, but in the form of crude sailors who should never be role models. Luke physically grows up, but mentally he never does, becoming one of the generals in the pictures on the walls at the orphanage. He is a hero, but not a person. A freedom fighter and a leader, but not a man.
Luke's world, as Peter Pan's, is then rocked to its foundations with the introduction of a female presence for almost the first time. (Femme-shaped fairies and bots notwithstanding).
Angela and Moira as Wendy Moira Angela Darling (I see what you did there!)
The introductions of Angela and Moira, almost on top of one another, is a distinct blow to the self-created image of Luke, just as Wendy is to Peter Pan. While Wendy is a child herself, and a story teller, and a maternal figure to her siblings, Peter Pan sees her as his companion. His partner of sorts, but not his equal. In so far as he, to the best of his knowledge and ability, is a "father" to his lost boys, she is to be the "mother," that he imagines. Luke is, similarly, a father-figure and leader of his soldiers and rangers, and Angela in particular is set up as a nurturing "mother" to these futuristic lost boys.
With Luke as patriarch of his (presumably?) all-male ship and possibly even an all-male squadron, Angela and Moira are enlisted to fill traditional female roles. Some might argue the maternal role of Moira, as she is a warrior in her own right, but I believe that as a moral compass for the group, she is completely comparable to Wendy. Angela, representing the sexual attraction that Peter Pan feels towards his Wendy, also brings to light the stunted growth of every "lost boy" under Luke's command.
Additionally, by creating Angela's Clone, the show creators have added an element of the foreign back into the feminine presence in this world. The robots that raised these Ranger boys have created another mother for them, and she is as much false and fae as they.
This brings the "rightness" and "humanness" of the real Angela into question, as Luke is unsure of her origins. Could she simply be a lost girl, at the whims of the robot parents, rather than the mother they all crave? Perhaps. Could she be a stand-in for Tinkerbelle, via her Clone, as the representation of all that they should and do want, but in a manner that they cannot and should not have?
And what of her relationship with Luke? At first he is wary, not wanting a woman on his ship, particularly in a position of leadership and power. Moira he allows a bit more grudgingly, because he is able to quantify her as "alien," as "other," and as a warrior in her own right. He accepts her as a native, rather than as a female from his own species. Moira is therefore initially acceptable, much as a Trojan virus is. She, from her interior position, may then begin to serve as his conscious, presenting these feminine aspects in a veiled manner that is initially acceptable to Luke.
Angela, however, is as foreign and "of home" as a body can be in space, and she is most clearly out of place on the space ship. Luke resents her immediately, as well he should, because she is being given a position of power similar to his. In fact, in certain medical situations, her power matches and even supersedes his, making her a threat to his masculinity and position as well. Thus, Angela is far less acceptable an addition to his crew initially. All of her offerings are taken as one would view a potentially poisoned fruit.
However, Luke soon notices his attraction to her is growing. Surrounded by men and bots for all of his life, and being confirmed as strait, unlike Ryan, he is unsure how to deal with his body's reactions. As with the pubescent Peter Pan, who has no idea how to handle the new reactions of his body, Luke is also in the position of prolonged exposure to a human female for the first time.
As her "wiles," as he calls them, but really just her general nature as foreign to him, begin to work on him, Luke falls under the thrall of her body. This is not to say that his love for her is unreal, or that her feelings for him are manipulative or undeserved, but that they are simply arriving at the same conclusions from two different paths.
Amalgamation as Hook and Dogfighters as Pirates
In Peter Pan, the main nemesis of the lost boys, led by Peter Pan, is Hook and his band of pirates. Hook is so named because of the damage dealt to him by Peter himself. Presumably he had a name prior to this interaction, but it is never revealed to the audience. In Ghost Soup, the obvious comparison is the Amalgamation. Interestingly, the first character in the Ghost Soup canon to actually use a name for the shadow figures we see is Luke, while talking to Ryan (another lost boy/ranger). Before then the villains were not identified, simply shown as figures causing havoc, and a dark planet ringed by misty veils. In battle, Luke blasts one of these ships with the cry of "die, Dog of the Amalgamation!" Thus introducing the name of the canon-wide villain.
In our comparison to Peter Pan, it is slightly tenuous to compare a shadowy, borg-like home planet to Hook, but I will explain. In addition to being an actual pirate, Hook is a personification of the terrifying kind of father figure that the author feared. A combination of rigid Victorian fathers and an over-regulatory government obsessed with conquering other lands, Hook is more of an idea than an actual pirate. As such, the Amalgamation comparison becomes more clear. The Amalgamation is, at once, a planet, a race, a coalition of other planets, a fleet of ships, and the individuals within them. An enemy that can be anywhere and yet far away at the same time, conquering without discernible motive, capable of punishing any ranger/lost boys that cross its path.
Luke's past has some glaring plot holes in it, but there have been hints since the beginning that he has more of a past with the Amalgamation than your standard ranger. Could he be somehow related to it? Escaped from it? Dealt it a terrible blow? … Cut off its hand? ;)
Additionally, the Amalgamation can be seen as simply the shadowy leadership on the misty planet – a metaphorical Hook – while the individual planets, ships, and dogfighters can be seen as pirates to the Ranger's lost boys. These elements meet and clash over and over through the seas of space, fighting a neverending battle.
This is their Neverland.