Genuinely surprised to see Sylux not being chosen at all.
Though to be fair, the road Arne takes to becoming Sylux in Saga is one of heartbreak and a deeply painful revelation about the people who scoured his homeworld to ruin for the promise of getting their hands on some Alimbic technology that he was not prepared to handle afte the Chozo and rather importantly for Skjoldr; Elmorni; were no longer involved in the lives of their charges.
The following is not really a Saga spoiler since this isn't treated as a dramatic reveal so much as it is an inevitable discovery; for one thing, the reader knows who destroyed the people of Cylosis long before Arne ever does. Think of it like how Anakin's fall into Darth Vader is treated, you know it's going to happen and the general gist of how it happens long before you ever see it happen. Besides, this doesn't contain a lot of the important details in the future chapters of Metroid: Saga that would actually be treated as surprises.
The people who scour Cylosis are of course, the Galactic Federation's Black Ops paramilitary outfit under the command of its intelligence service rather than its military chain of command or civilian government; the Rapid Armed Intelligence Division or R.A.I.D. Whose basic soldiers are basically Astartes+1; more than three meter tall posthuman power suit clad bioborg killing machines with automatic mini-missile launchers as standard issue meant to be able to fight mainline space pirates; who based on model scaling are 11-13 feet tall; with individual superiority rather than the Federation's usual tactics of greater numbers and heavy reliance on vehicles. And of course, outmatch other combatants like Kriken Soldiery, Omdyni Mech-Grenadiers, or Vhozon Confessors.
Though Samus doesn't know of them because the R.A.I.D is a deeply buried secret to the point of not even officially existing and having a completely off the books R&D and logistical/industrial complex and chain, when Arne finds out about it after most of the resusticated Alimbics are wiped out again by a betrayal from within the ranks by the anti-Arne faction of Almbics and the Zebesian Chozo get plastered by Mother Brain betraying them to the Space Pirates after obscuring their visions with her psychic powers he assumes the worst. It goes down shortly before zero mission just after their seventeenth birthdays; a bit less than two years after the betrayal; Arne finally finding what the RAID really is; no longer knowing who to trust after having had some severe downspirals, and just leaving Samus and ghosting her to let her think he killed himself so he can face the Alimbic faction that was against him before its partnership with the RAID bears fruit in a way that would radically alter the balance of power. Leaving Samus to go return to Zebes on her own to do battle with Mother Brain and Ridley.
Both face their betrayers and their new allies made from the people who orphaned them. Samus merges the Ancient Chozo armour that was always made to be acquired by her with her own suit to grow her understanding of ancient Chozo technology; Arne acquires the Armour of an Alimbic Paladin and more importantly; the Sylux armour designed by the traitor Alimbics as part of a suite of inventions meant to provide the means of bolstering their combat capability to progenitor levels. Arne takes the name of the Armour and assumes his new identity and remains in it for years; hiding himself out of shame and an incredibly unhealthy mix of emotions he's not in the right headspace to handle. He doesn't become evil so much as broken and lonely, having failed to deal with his childhood trauma the way Samus did and becoming a lesser, darker hero than her for it.
In Saga, it'd take years for the actual truth to come out and reconciliation to begin, here, you can stop his fall from ever happening to begin with. Just make sure his mental state remains in good condition and make sure he gets friends. He's not only an orphan, but a victim of severe physical and emotional abuse from Zurvduat who not only never loved him but came to hate him for being; in the general's opinion; soft. An overly sensitive crybaby overly attached to the legacy of the corpses of his birth parents, always reading through the texts Gyda and Erik Skjoldr wrote on politics, philosophy, guerilla warfare, sociology, and more that Elmorni; chief of research on the Alimbic ship that Arne's parents uncovered and accidentally revitalised; encouraged him to indulge himself in to grow a connection to his human side.
Zurvduat's hatred was only further worsened because his actual biological children all died when Gorea devoured the Alimbic Tetrarch Order; and he woke up to a universe where the country he served and the family legacy he cultivated for hundreds of thousands of years was all dust in the wind for the last fifty thousand years. Despite all the man hours he spent searching, he never found any proof that any of his offspring reached safety in stasis, and now he had to raise a sniveling smoothskin whom Elmorni continually sabotaged his attempts to try and make a simple, pliable philosopher-soldier and a template for human-alimbic hybrid soldiers to help rebuild the empire with their hugely depleted manpower. And perhaps even one day being useful bodies for the countless disembodied Alimbic telepathic essences left by the sudden, traumatic demise of the whole of the Alimbic species; such as say, his eldest and most favoured son.
So Arne's a pretty broken person who has a black hole of trauma in place of a proper father figure and has a tendency to wilt from pressure from people who remind him of Zurvduat on top of his terror from Cylosis' demise. He's desperate to please people he likes, tries to not bother them with his problems if he can help it, continually insecure regarding ever displaying any signs of weakness from his person, and constantly doubting himself. Being put through training like running the same six-hour long (not six hours from his accelerated perspective of time, six hours from our perspective of time so it's even longer for him) combat scenario again and again, having to repeat from the very beginning any time he made a mistake as small as overkilling a single drone, for five days without pause or rest, made him into a neurotic mess of self-criticism.
Samus' problems are more to do with her tendency to be overtly selfless and need to just help everyone in sight. An obsession with fixing everything she can to try and make it so nobody goes through what she did on K-2L ever again. She doesn't know how to take a breather, while she criticises Arne for not thinking about himself enough, nobody pushes themselves quite the way she does to try and help out others. She's the kind of person who spends endless hours thinking about how they can help solve everyone's problems large and small and will spend whole months without getting enough rest or down time just trying to find out how she can save either the multiverse or just some people she thinks are down on their luck. She's burning the candle at both ends and tends to be very reluctant to let other people take her burdens unless she's absolutely sure they can take care of themselves. She's afraid of losing people, and worries herself deeply every day over how all of her friends are doing.
Which also leads her to not make too many, because she can't help but worry. Even for people who definitely can take care of themselves like Arne. She resents restrictions placed on herself and yet is one of the most protective friends you could have. If she doesn't think you can take care of yourself she's not likely to let you go very far without giving her assurances. Which makes her distant from normal people because they're all so fragile. It also means she tends to not like to be supported by large number of more mortal allies because she'd worry herself sick over the possibility of mass casualties from people who aren't able to take punishment the way she can. Not unless there's something done to let her take her mind off of their fates. Something to make them less fragile, less vulnerable.
She's a free spirit, but needs to learn that it's okay to spread the burden and that it's okay to let people take risks. She's able to handle it for now because she's still in the "oooh, aaah" stage of things, but once things start to sink in to her she's going to freak at the idea of people who can barely squeak to a century of life throwing away their lives in this kind of combat and will be sinking herself into trying to hold the weight of the omniverse on her back. So far people have avoided serious, mortal injuries, but that's not going to hold forever, and as smart as she is; she's a not super well adjusted teenaged girl who's been outside of a restricted social circle comprised entirely out of some of the remaining progenitors and some handfuls of youths for maybe a whole year in total.
She also has a temper and often responds to her trauma by trying to bury it in rage when something she can lash out at triggers it. When she's in an episode, she will break things, she will scream, she will just go absolutely frenzied in an attempt to try and distance herself from the sensation of helplessness she felt on K-2L. In a vision where she can't really do that she is at least, manageable. When she's in more of a capacity to try and punch her way out of things, you better hope you've got a holodeck handy for her to go full on "hulk smash!" in or at least, a lot of things to break you don't mind losing. She builds a lot of dumb A.I training robots specifically to have something to fight and break when she's got an episode going on. That sense of fear of powerlessness also drives her to push herself to self-improve and try to push for being the best she can be at all times.
It's why she doesn't go into missions with more than a tiny portion of her gear unless absolutely needed; she needs to prove she can manage even with a stripped-down arsenal and just what she can find. To prove that she could stop another K-2L with her bare hands if need be. Arne does it because he doesn't bring in equipment he feels that the current deployment doesn't warrant; fearful of overkill following year after year of abuse to make him more "efficient". Samus does it to prove a point. That she can handle it, she can save people, that she can help people even if she doesn't bring in her a-game.
