Soul Nomad and The World Eaters/WMG

The Dracon race are directly descended from Drazillians.
Both act insanely arrogant. They possess strikingly similiar fashion sense, though the Dracosages' robes have less impressive Shoulders of Doom. The Dracon appear to worship evil Gods, and draw their power from them. Then there's Dio and his aspirations of practical Godhood. A World Eater even gleefully rants about how delicious a Dracon's soul is, and specifically refers to now possessing said Dracon's power even though he devoured several other souls at the time...
 * Not to mention the optional scene where Danette plays with Odie's manikin and snaps his neck, with apparently no major (read: long-term) side-effects...
 * In Father Valerio's sermon on the origins of the races, he refers to the Dracon being born by lightning cast by the gods. The Dracon are (supposedly) superior to all of the past races, learning from their mistakes; however, they also grow too obsessed with the past and ignore the future, to the point that they are completely unable to cope with change... a flaw shared by the Drazillians. Presuming that his sermon has some basis in fact, the Dracon could well be an early attempt by the Drazillians to impose their will on Haephnes, crafted in their likeness and fully expected to thrive by following the Drazillians' ideology exactly...
 * Um, since when are Drazilians arrogant? Their gods, sure, but the Drazilians themselves are pretty much the exact opposite of arrogant, having no individuality and thus no sense of self-worth. Also, there's no indication that any Dracons other than Kanan and the rest of the Thurists worshipped anything but the gods of Apis, same as everyone else. And Dio is pretty much the only Dracon who's shown to be particularly arrogant. Most of the Dracon NPCs found in the various towns and cities come off as a bit reserved, but generally friendly.
 * Were you paying attention to the end of the game? All the Drazilians looked down on Layna, and indeed anyone who isn't a Drazilian. Not to mention the heads of the Drazilian world tried to program Gig to destroy the earth world.
 * I might ask the same question of you. They weren't looking down on her; they honestly thought that anyone who didn't look like them was deformed, which wasn't an unreasonable assumption, given that they'd never seen anyone who didn't look like them before. Furthermore, their initial reaction to her (to try to 'help' her, as opposed to driving out the 'freak') is, under the circumstances, about as far from arrogant as you can get. The 'heads' you refer to are the aforementioned Drazilian gods, who were responsible for brainwashing them into that state, and were indeed exceedingly arrogant. And all of this still doesn't address the fact that the Dracon as a whole do not show any signs of either being particularly arrogant or of worshipping any differently than the rest of the races of Prodesto.

The actual canon path is the Demon Path.
And much like Phantom Brave before it, any crossovers with later games are going to turn out generally worse for the poor cast.
 * Jossed by Disgaea 3. Gig and Revya (a female Revya, at that!) appear in the post-game quest as separate characters with their own bodies. All of the good endings on the Normal Path incorporate this idea in some way, whereas both of the Demon Path endings contradict it. Danette's cameo in Revya's Holy Justice attack drives the point home, as that attack was only available on the Danette-friendly Normal Path.
 * They're downloadable content though. Characters such as Human Kurtis and Frog Tink also appear as DLC, so not all (if any) of the DLC is canon.

Crimson Tears are a lesser form of the Philosopher's Stone from Fullmetal Alchemist.
Both are red crystals that greatly enhance their respective series' Functional Magic and are composed of human souls. The main difference seems to be that Crimson Tears are composed of only one soul (thus dissolving after being used once) and can form naturally (relatively speaking) while the Philosopher's Stone is composed of thousands of souls and can only be created deliberately.
 * Given that FMA is six years older than Soul Nomad, it seems likely it was, at least, a major source of inspiration. I'd contest the 'lesser' status as one crimson tear (albeit a very potent one) was able to form an inter dimensional portal between Haephnes and Drazil, and another one was used to bind a god to the soul of a human.

Raksha and Thuris are actually Gig and Revya.
This mostly has to do with the "good" Lord Median ending. In this ending, Gig & Revya travel back in time; then Revya contracts Scarlet Iago and dies. Their two souls are captured by Drazil, who says three important things: First, that he already received "a Master of Death from Haephnes a few months ago", second that he will "finish the souls' fusion and then pull the souls apart completely", and finally that he has "two openings for souls to be made into powerful weapons". So the "original" Gig is accounted for and we know Feinne is Resilience, but nowhere else in the game are Raksha and Thuris' origins explained. And what is Thuris known for? Scarlet Iago!
 * As the Stable Time Loop entry states, I don't think you're alone on this. In fact, I thought it was outright stated by the game (Presuming Raksha is Gig, because he's more powerful, and Thuris is Revya because of the Scarlet Iago connection).
 * Alternatively, assume Thuris is Gig (murderous psychopath who does it For the Evulz), and Raksha is Revya (sick and tired of being an Unwitting Pawn for his entire existence). Sure, it adds disturbing implications to female!Revya's ending with Levin, but the personalities line up better.
 * For the above two, probably both. Drazil himself stated that he waited until both souls fused together, meaning when the result was split, the two parts contain elements of both characters.
 * Personally, I've always assumed that he used them to make Gamma and Joules.

Odie knows how to handle guns.
Endorph taught him while he was training the angels, for safety purposes. Odie doesn't use them normally because of his insecurities: he feels that he can't match his master's skill, and besides, he's a mage... or trying to be one, anyway. Using firearms seemed like a crutch. (Plus, it would derail the plot if he just shot Revya.) However, once Nippon Ichi has him cameo in another game, and he sees that spellcasters using shotguns and other weaponry is perfectly acceptable...

The Demon Path is Layna's personal Purgatory.
Following her death at Raksha's hands, Layna/Virtuous is thrown into a Drazil-influenced Purgatory and forced to witness a world where her Xanatos Gambit went horribly wrong. Revya doesn't just call her out and refuse to go along with her plan because that wouldn't be terrible enough; no, he/she has to turn out to be an Ax Crazy psychopath who promptly takes a running leap off the Slippery Slope and picks up where Gig left off. Instead of raising a hero, she's created a monster and given them power that is practically unmatched. All of the other horrors, such as Trisha's fate, are meant to torture her further -- Trisha may represent all of the other "daughters" that came before her, or other innocents who lost their lives while she was biding her time.

Danette and Layna's survival may feel a bit Deus Ex Machina, but it's due to Layna finally deciding to fight back against the nightmare. Similarly, the Heel Face Turns are due to her regrets, acknowledging that they would have made fine allies. If Revya claims that he/she wants to go back to the way things were, Grunzford launches into his massive What the Hell, Player? speech; this is actually Layna forcing herself to acknowledge that she can't restore this nightmare to the way it 'should be', and her regret over manipulating them. Danette's Heroic Sacrifice is salt in the wound; surely she considered the possibility that she had the potential to become a Crimson Tear before... The bad ending takes the worst case scenario all the way to its logical conclusion, while the good ending is Layna taking control of the nightmare anyway and dealing with the problems she created at great personal cost, following which the real Revya and Danette defeat the Drazilian Gods, allowing her to escape Purgatory and return to life.

Reyva is Baal
Follows "The Demon Path is Canon" idea. Baal is an almost obligatory Bonus Boss at this point, so why is he(?) missing? Because 'Baal' hasn't existed before the rise of the Devourlord. And with all the Prinny incarnations, it's pretty safe to assume Baal did something moderately horrendous. Like destroying and consuming two separate worlds, maybe?
 * Jossed. Soul Nomad takes place 10 years after Phantom Brave, making it the last known game in the Nippon verse time line. Baal has been around during Phantom Brave.
 * Except that Lujei was able to influence matters in Phantom Brave, bringing Sulpher back to the world. Even counting that she's a 'time witch' travelling dimensions, the fact that she's the root cause for basically the majority of the situation in Soul Nomad means it cannot be discounted entirely. 'Timeline' doesn't mean much because of the circumstances.

All the Normal Path Epilogues are canon
Danette, Virtuous, and Grunzford return to the Hidden Village. Layna is set up as a possible temporary World Ruler for the now godless Drazil. Vitali opens the restaurant. Tricia takes over what's left of Shauna and Endorph's band of thieves and becomes Just Like Robin Hood. Odie takes Dio's place as head mage of Orviska and helps Vangogh with his hotpod farming business. Endorph and Euphoria end up together and have a child. Levin/Raksha somehow returns and simply decides to Walk the Earth, Becoming the Mask. Juno decides to settle down and take care of the newborns at the Nereid's Palace. And Gig goes on a search for the Golden Hotpod, all while trying to steal as many hotpods from everyone else. As for Revya, he/she most likely returns to the Hidden Village to duel with Danette and search for the Golden Hotpod with Gig.
 * I believe this as well. The endings could just explain what everyone's up to. This would mean that the most likely canon endings are either the Danette or Gig ending.
 * This is proven for the most part by what Grunzford says in the Male!Revya ending with Gig.

The events of the Normal Path and it's ending is the culmination of a very long Groundhog Day Loop
Haephnes used her power to constantly reset everything to prevent her world's destruction and bring balance back to the stream of soul after Drazil disrupted it. However, not everything resets perfectly thanks to interference from an outside source (*cough*Lujei Piche*cough*), sending one of the incarnations of Revya and Gig to the past, causing the above WMG about how Raksha and Thuris were created from the fused and split Revya and Gig.

Bonus content for a hypothetical Updated Rerelease
Since they've remade many other games already. The bonus content will likely create an entirely new path:
 * A crossover with Makai Kingdom. Since Asagi left Zetta it makes sense he'd follow her when he could. Possibly bringing Salome and Alex along (well, Alex wasn't really brought along). Oh, and Zetta's out of the book! The real reasons for this - besides the hilarity of Zetta and Gig snarking at one another - are twofold.
 * Castille tags along for her touching reunion with her brother.
 * It allows Gig to be a playable character while being sealed in the sword...the same way Zetta was playable while being sealed in a book. Yup, Baal's here, and he's taken Gig's soulless body as his own.
 * This builds up to the Bonus Boss against an entire army of Baals and Prinny Baals. It will be epic.
 * Oh, and Demon Revya would show up at some point, and good Revya would have to fight him/her.
 * I do remember something mentioned on the original Japanese site about a cellphone game that detailed Layna's confrontation with Virtuous and how Layna eventually agreed to let Virtuous fuse with her. Perhaps a Layna Mode?

Revya is a Dark Signer in the Demon Path
In the Demon Path, Revya did not survive the fusion with Gig's soul and died. However as Gig was actually Earthbound God Wiraqocha Rasca, and sensing the lust for revenge in Revya's heart (Which may have been caused by being The Unfavorite of Layna, as she always supports and cares about Danette, but rarely mentions her own name), he decided to turn her into a Dark Signer. Revya's actual goal in the Demon Path is to ressurect Gig like the usual Earthbound God: By sacrificing Souls, except that this time, they're doing it manually. In the Bad Ending, they finally sacrifice enough souls to summon Gig... However, at that rate, Revya was far stronger than him, so she devoured him and obtained enough power to cross to the other world, and destroy all of existence because it was FUN
 * In fact... Maybe Revya is not the only Dark Signer. Everyone who joins her is. Galahad and Kanan were killed in battle, but were spared by Cusillu and Aslla piscu respectively. Thorndyke, Cuthbert and Shauna allowed Revya to kill them and were spared by Ccapac Apu, Uru and Ccarayhua. The only exception is, who was lucky enough to keep his life, as Chacu Challhua did not see him as worthy, so they decided to keep him around so he can be The Evil Genius.