The point is that, for as detailed and well founded as Warhammer 40,000 is, readers tend to be invested in the unknown. Whether it's the fate of the Ordo Chronos or Cypher's true allegiance, the ability to have a well founded but extremely malleable canon has served the lore well over the decades. There are a hundred unanswered questions, theories, quests and half-hidden truths throughout the Adeptus Astartes alone, and a fair number of chapters were even built upon such half hidden answers; the Grey Knights being the quintessential example of these armies. While the chapter has seen some exceptional stories (Ben Counter's trilogy) and some exceptionally bad lore (take a wild guess) one recent question has kept fans hungering for answers - Who was their first Chapter Master? Who was Janus?
While we admittedly only know a few, very limited, details about just who the leaders of each chapter were following the Horus Heresy, Janus was a special case. His chapter had no direct link to a prior legion or legacy from that war, little was made clear about him save for his importance and name; but most pressing of all were his origins. Was he a new recruit, someone trained to lead this chapter from a young age, or was he a survivor of the Great Crusade? More importantly, if so, was he even a member of the loyalist legions?
One very popular theory for a long time was quite a curious choice - Many claimed that Janus was, in fact, Omegon. Recognized as the hidden twin of Alpharius, a number of Horus Heresy tales had depicted the primarch undermining the Alpha Legion's efforts. Apparently more willing to directly assist the Emperor's legions than Alpharius, a few short stories even suggested that his conflict was bringing the legion to the brink of civil war. Naturally, fans leaped on this and started joining the dots.
These ranged from the meaning behind certain names (Janus in particular was a Roman god of two faces, emphasizing the beginning and ending of things I.E. Alpha and the Omega etc.) to picking out certain new details. In the (absurdly excellent) Mortarion's Heart, the Death Guard daemon primarch hinted at something dark in Janus' past, all but outing him as a former member of the Traitor Legions. There were whole essays written on the subject, quite well researched and intelligent ones, which pieced together countless details to suggest this was all but inevitable.
Unfortunately for the fans, they turned out to be rather wrong though. Praetorian of Dorn threw a rather large spanner in the works, not only forcing Omegon to take Alpharius' place but strongly suggesting that he would remain adamantly loyal to Horus' traitor forces. Combined with a surprise death, it all but confirmed that Omegon's place at the head of the Grey Knights was impossible. This was something which irked some groups to no end, and probably would have created a minor firestorm of fan-rage were it not for John French's outstanding penmanship.
Of course, this leaves the big question now - Who exactly was Janus if not Omegon? Many think that this would be Nathaniel Garro thanks to Mortarion's comments, and this would make sense. Garro was an experienced Captain, he held a distinguished position among the Knights Errant, and was trusted with a number of extremely tightly guarded secrets. That said, while he would certainly take a prominent position, there are character traits which clash with this theory. For starters, Garro was far more morally upstanding than many of his contemporaries, to the point where he actively opposed killing innocents even when the situation demanded he do so. Not exactly a character trait which befitted a Grey Knight. Furthermore, he was a staunch traditionalist and, while the Imperium slid backwards somewhat, the new age also demanded a very different kind of leader to guide them. Combine that with his unwillingness to keep too many secrets hidden from his allies, and his reputation as a frontline officer with a few minor micromanaging issues, and he doesn't seem like Chapter Master material.
Instead, we need to look at some else. Someone important to the series who was both a member of the traitor legions, a proven captain and a level of objective ruthlessness balanced by self control few could accomplish. We need to look to Garviel Loken.
Now, let this be clear: What's going to follow is as much a mixture of guesswork and estimations as the Omegon theory. A great deal about this makes sense, but at the same time it could easily be disprove thanks to the story going in another direction. That said, this would thematically and personally make a great deal of sense. For starters, Loken is someone who has already abandoned his name once. Becoming the madman "Cerberus" following the Isstvan III Atrocity, he all but completely buried his original persona beneath a new identity; one he required to help defend himself amid the hostility and insanity of that conflict's bloody aftermath. When he returned to being "Loken" he was still shaken to the core, to the point of practically feeling fear as a mortal would and wasn't the same man. Unlike Garro, Loken seems like a figure who would more willingly accept a mask, and even erase his original name.
Loken was also much more willing to work with his subordinates and offer them tasks he would personally perform. During Horus Rising and Galaxy in Flames, the battles there depicted him readily turning to his Sergeants and fellow Captains to coordinate attacks and perform vital duties. While more often than not serving on the frontlines, he knew when to step back and allow for others to take his place. In addition to this, in keeping with Mortarion's comments about Janus retaining a high rank within a traitor legion, Loken did have the Warmaster's ear at one point. He was valued enough to be offered a chance to return to the Sons of Horus despite all that had taken place, and even displayed an uncanny ability to combat daemons he encountered.
More-so than anything else though, Loken's role as Janus would fulfill a certain thematic quality for the series. Loken introduced the Horus Heresy books speaking of being there when "Horus slew the Emperor" in jest, and witnessing the end of one era. Taking on another guise, leading the Imperium's new forces into a darker age while fighting for the light, perhaps even speaking to new recruits of the Siege of Terra; it would be extremely fitting for the opening words of the series to be the same closing lines at the end of all of this. Perhaps there would even be a chance for him to reflect upon whether the Grey Knights could succeed where the old legions failed, or even seeing something of the Luna Wolves in them.
This is, of course, just one possibility. There are countless others which have been discussed, from Saul Tarvitz (because some people will simply not accept he is dead) to Rogal Dorn, but Loken seems to make the most overall sense. Still, if your own suggestions or theories, please feel free to list them in the comments of course. It's been quite some time since we've had any lengthy discussions over the lore.