It's my opinion that a vast majority of people that I've spoken to about the New Jedi Order series have completely misinterpreted it, largely due to Traitor. Which isn't to say it's Matthew Stover's fault, because he clearly has said what he was going for, and part of that is to let people draw their own conclusions about the book, untainted by authorial intent. I'll preface by stating that I haven't read any of these books in several months if not longer, but I'd like to think I have a pretty good memory. And I suspect if I did re-read Traitor, my interpretation would probably shift slightly, as it seems every time I read it a new idea is discovered.
That said, I'll start with Traitor. The book itself is entirely about epistemology. We only get three POVs in the novel: Jacen, Nom Anor, and Ganner Rhysode. Vergere's POV is never depicted; consequently, the reader is left, along with Jacen, to determine for themselves the veracity of her claims, as well as discern her motives. The book switches toward the end with Ganner's perspective, casting Jacen in the same light, thus sort of providing a guide by which we attempt to discern Vergere's intentions, at least in the sense that we have some degree of understanding to Jacen's thoughts from his POV, and can get a better handle on Ganner's POV of Jacen.
Ultimately, the most important information communicated in the book occurs in the Solo apartment and in the epilogue. In the former, Vergere says "Ask yourself. Where else can one look?" That's essentially the entire lesson Vergere is trying to teach Jacen, about epistemology and knowledge. In the epilogue, she then tells him about compassion, which I think is important but isn't her main lesson: "You need not like someone to love him. Love is nothing more than the recognition that two are one. That all is one... That knowledge is the seed of greatness."
The Jedi are predicated entirely upon compassion, and I think Vergere has really hit it on the head even more than Obi-Wan and Yoda did. Incidentally, this also ties into The Unifying Force down the line, along with her apparent assertion that there is no dark side.
Now, onto Destiny's Way, where she talks to Luke as an equal, explains her intentions with Jacen and what she was doing to teach him, ridicules the Potentium Perspective, and acknowledges that the dark side exists! I actually find Vergere's discussion with Luke potentially "darker" than anything she says to Jacen in Traitor, because the sincerity with which she says anything in Traitor is entirely up in the air. But with Luke, her discussion concerns the dark side, and whether anger and aggression, and acting upon these emotions, is specifically dark, or only if one acts with them in a way by which they dictate one's actions. Thus, she seems to be walking a razor thin line with regard to what we know about the Force, but also one worth questioning. At one point at TFN, Stover posed an interesting question: was Yoda perhaps overly cautious in training Luke due to his father's mistakes and the potential for Luke to repeat those mistakes? Perhaps Yoda didn't want to take the training wheels off the son of the Chosen One because doing so with the Chosen One had not worked out?
Vergere tells Luke: "Our difference concerns where this serenity originates. You believe serenity is an absence of passion, but I believe it is a consequence of knowledge, and self-knowledge most of all."
Luke replies: "If passion is not opposed to serenity, why are they paired in the Jedi Code?"
Vergere states: "Because the consequences of these two states of mind are opposed to one another. An unchecked passion produces actions that are hasty, ill considered, and often destructive. Serenity, on the other hand, may well result in no action at all -- and when it does, serenity produces actions that proceed from knowledge and deliberation, if not from wisdom."
As for her actions in Traitor, Vergere explains what she was doing: "Jacen Solo had to be bereft of friends, of relatives, of teachers and knowledge and the Force and everything that could help him. He had to be reduced to nothing -- or rather, to himself only. And then he had to act -- to act purely out of himself, out of his own inner being. In that state of complete disinterest, everything else having failed him, he had no choice but to be himself, to choose and to act."
Based upon the premise that Jacen was left "bereft of... teachers and knowledge," it's my conclusion that Vergere's means of doing that, since she quite clearly offers him information about the Force, is that she fed him both true and false information, leaving him to figure out which was true and which was false. And thus, I'd say the reader was also left to figure out when she was being sincere and when she was being insincere. It would appear that since most people believe that Vergere proposed the idea that there was no dark side, that they believed she was sincere when she proposed this. Given that she freely discusses the dark side with Luke, I would think it obvious in retrospect that she did not, although I do think there was some truth to it "from a certain point of view," which will make sense come The Unifying Force.
As for The Unifying Force, I think the full context of the "boon" of Jacen's hero's journey is better understood with more information on what the "Unifying Force" actually is. Introduced in Episode I, albeit indirectly in the film and slightly more directly in The Making of Episode I and the film's novelization. George Lucas defines it in the former as: "The Force itself breaks down into two sides: the living Force and a greater, cosmic Force. The living Force makes you sensitive to other living things, makes you intuitive, and allows you to read people’s minds, etc. But the greater Force has to do with destiny. In working with the Force, you can find your destiny and you can choose to either follow it or not."
The Living Force is the Force that is divided into light and dark, while the Unifying Force is essentially the "source," the "gestalt" or "whole" Force, untainted or unfiltered as it were by life into those two sides. It is the source of the will of the Force; as there's no "dark will" that emanates from the dark side, likewise there's no "light will," there's only one will which emanates from the Unifying Force. This was further exemplified in the Mortis trilogy of TCW, in which each of the three Force wielders embodied an aspect: light, dark, and the Unifying Force.
The Jedi are all about balance. The dark side in the Mortis trilogy is about destructive impulses, disobedience, and selfishness, while the light side is about creative impulses, obedience, and selflessness. The Jedi need to employ some destructive impulses in their work such as "aggressive negotiations," and I'd argue that things such as disobedience have their uses in certain situations. The idea of Jedi seeking balance is also echoed in a lot of the prequel era Expanded Universe literature, such as Cloak of Deception, which has a few good quotes that echo the Mortis trilogy:
"It sometimes seemed to Valorum that the Jedi behaved as if the Force ruled the ordinary world, and that the role of the Jedi was to behave in such a way that a balance between good and evil, light and dark, was forever preserved -- lest the scales tip one way or the other, opening a portal for the dark to come streaming in, or for allowing the light to blind everyone to some greater truth."
Thus, the chief concern of the Old Republic Jedi prior to the prequels -- especially with the believed absence of the Sith -- was not that of loyalty to light over dark, but of preserving the balance and to the greater unity of the Force and its will. This wasn't impressed upon Luke by Yoda or Obi-Wan, as one idea proposed during the NJO, or possibly I, Jedi?, was that Luke was trained as a weapon against the Sith. His training did not deal with the Unifying Force at all.
Thus the purpose of the New Jedi Order series was to reintroduce this idea to the New Jedi Order. And so, The Unifying Force concludes with Jacen realizing that the reason he could sense the Yuuzhan Vong via Vongsense was due to their latent connection to the Unifying Force, the Force beyond what the Jedi could sense and something which could not be stripped from them, since life and the Force are innately connected. And he achieved union with the Unifying Force completely during his battle with Onimi.
As well, Jacen and Luke discuss what Vergere said about there being no dark side, and decide that it is wrong:
"It's true that the Force is unified; it is one energy, one power. But here's where I think you and Vergere are incorrect: the dark side is real, because evil actions are real. Sentience gave rise to the dark side. Does it exist in nature? No. Left to itself, nature maintains the balance. But we've changed that. We are a new order of consciousness that has an impact on all life. The Force now contains light and dark because of what thinking beings have brought to it. That's why balance has become something that must be maintained -- because our actions have the power to tip the scales."
I find it slightly problematic that Luke attributes the belief of no dark side to Jacen, because as far as I know he never proposed it himself and merely relayed what Vergere told him, and I also don't believe Vergere was ever sincere in stating it so much as it being a rhetorical question of sorts for Jacen to ponder due to her discussion of the dark side with Luke. That Luke seemingly forgot this I chalk up to multiple authors writing in the same series. Speaking of Vergere's apparition:
JACEN: "Maybe she learned to tap into a power that was more all-embracing than the Living Force."
LUKE: "The Unifying Force. That might explain it. In fact, all the years since the deaths of Obi-Wan, Yoda, and my father, I've felt as if the Jedi have been on a quest to recover the Force's power to glimpse the future, which is perhaps the nature of the Unifying Force. The search has not been unlike our search for Zonama Sekot. And there's a power here, in the air and the trees and everything else, that convinces me we've found our way to something even greater than what we were seeking."
Sekot instructs Jacen on the Unifying Force:
"Jacen, to tap deeply into the Unifying Force, we will have to surrender our desire to control events. We will have to unbridle ourselves of words and of thinking, because thoughts, too, are born of the physical world. We must refrain from analyzing the Force, and simply allow the Force to guide us. Our relationship with the Force must be impeccable, without the need to be supported by words or reason. We must carry out the commands of the Force as if they were beyond appeal. And we must do what must be done, no matter who attempts to stand in our way."
Luke, after the conclusion of the Yuuzhan Vong War, says to the Jedi Order:
"But here's what I wish to say to all of you: if I have learned anything from the events of the past five years, it is that the Force is more all-embracing than I ever realized. Light and dark do not always stand opposed, but mingle with each other in curious ways. More important, the Force seems to have a will, and it's when we're acting against the will of the Force that we can get into trouble. Anger by itself is not of the dark side unless it is accompanied by a desire to dominate. When we act in harmony with the will of the Force, we disappear into it. When we struggle against it, we not only sever our ties with the Force, but also feed the needs of chaos.
"Our forebears believed that they could balance light and dark by remaining always in the Force, and thereby perfecting themselves. Gradually, however, as the Supreme Chancellors appealed to the order time and again for advice in resolving disputes, the Jedi became adjuncts of the Old Republic, then marshals and warriors, taking it upon themselves to uphold the peace, and little by little being drawn away from the Force and into the mundane."
Finally, Sekot itself states that it does not follow the Potentium, which I'm merely quoting so that it's not conflated with the beliefs espoused by Sekot or other characters: "The unprovoked attack by the Far Outsiders stirred something in me. Counter to the teachings of the leaders of the Potentium, I became aware of the existence of evil. In a sense, evil helped give birth to my awareness. Now I understand that the acts of the Far Outsiders may have been nothing more than a reawakening of the evil my parent experienced when its symbionts used its creations not merely to defend Yuuzhan'tar, but to launch an era of bloodshed that resulted in the death of countless worlds -- along with many latent planetary consciousnesses."
So ultimately, the "boon" that Jacen discovers in the New Jedi Order series is the rediscovery of the Unifying Force, and his moment of transcendence with it and rediscovery of that by means of his complete surrender to the will of the Force. The books set chronologically after The Unifying Force, starting with The Joiner King, sadly have completely ignored that aspect of the series, and instead became caught up on Vergere's claim that there is no dark side, an idea that I cannot find Jacen or Luke ever supporting at any time in the New Jedi Order series.
And thus, it feels as though the New Jedi Order series has become wholly irrelevant in that it has been rendered thematically moot by the reframing of its story to that of Jacen being seduced to the dark side by a Sith.
Post Script: This was mostly written stream of consciousness and I haven't re-read it in its entirety so it's possible that I left some idea open with the intent to revisit it and never did, so feel free to point out if I did, or request clarification, and it shall be done. Although, to be honest, I probably shouldn't have any sort of expectation that anyone will read this far.