Major Spoilers Ahead! Read At Your On Risk!
Mystery 1: Where did ARMs come from?
Theory: The Metal Demons made them/had them first. There is some evidence that they could have been originally the Metal Demons, and that the Elw and Humans simply took what they could get away from them. What's the evidence? Well...
Then again, this cannot be proved for certain.
Theory: The Elw could have made them. However, there is one flaw in this theory. The Elw create technology laced with magic. Rudy, however, is about as magical as a rock. If there was magic involved, don't you think it would take MP to use an ARM? Then again...
Mystery 2: Why were the Holmcross made of living metal?
Theory: It was for better ARM syncronization. If the ARMs originally belonged to the Metal Demons, then wouldn't it make sense to try to make one meant to use lots of them as close to the demons as possible?
Theory: The Elw wanted to make them helluva tough! *Dodges bricks* Er, rather, they wanted them to be made of tougher stuff than humans so they could survive anything.
Bean expands on this:
This kinda goes with the second one you had, but maybe because the Demons were made of metal. Metal is really hard to damage (Well, some metals aren't, like tin foil and soda cans [Chibi's note: It might be strong if it wasn't made so thin...]) and since the Metal Demons (being metal) might have been stronger than regular flesh-and-blood humans (and Elws?!), the latter wanted to make a weapon that could fight back and be tougher against the Demons.
(Thanks for contributing! ^^)
Theory: Maybe both theories are correct.
Mystery 3: Why didn't Lucied lose her power along with the other Guardians?
Theory: It was probably her connection to the demons, but still, how would that work? Demons or no, wouldn't you think the war wouldn't have weakened her as well? Or is it that Boomerang has enough thoughts of desire for her to feed off of so she can retain her power? Very peculiar...
Silver's Theory: Whatever weakened the Guardians attacked them through the Ray Line, and Luceid was never part of the Ray Line. (There's a hole in this theory, since Lucadia says the Ray Line was formed after they were weakened, but it makes a whole lot more sense the other way. Before the war the Guardians could've used the Ray Line to spread their powers throughout Filgaia).
Mystery 4: While we're on the subject of the war, what happened to the Guardian Blade?
Theory: It destroyed itself. Belselk hints at that in the Volcannon Trap. However, if it did that, then why did Mariel mention using it to save Rudy's arm?
Theory: Vassim still posseses it. But if he does, they why the hell would the Elw let him stay in their dimension when he could potentially frig up their dimension with it like he did Filgaia?
Bean's theory: This isn't really my theory though, but on a FAQ I read a while ago, someone asked about the Guardian Blade. The explanation was (I think) that it was possible to get it (I think in The Abyss), only it had another name.
Mystery 5: Why was Mariel exiled rather than Vassim?
Theory: The Elw wanted to be able to keep an eye on Vassim, but didn't want the crime of frigging up Filgaia to go unpunished. Still, hurting poor, innocent Mariel like that... That's not nice.
Theory:: The Elw are idiots. Rather, they lack common sense. Why would they want Vassim in their dimension if he could spell their doom?! Baka, baka, minna baka!
Bean's theory :Maybe the Elw had a society where the whole family would be punished for something that one person did. Like, if an Elw did something really bad, (like creating a sword which caused a large desert to appear and causing who-knows-how-many deaths [But he got the Demons to go away! Yay!]) maybe the Elw thought that the 'blood' of that Elw was bad and since the rest of the Elw's family had it, they should be punished before they did something bad. We can't be sure because we don't know about the type of society that the Elw had. (I think I'm thinking too much into this, though)
Silver's Theory: About why Mariel was exiled instead of Vassim...
First of all, I agree with FBD that the Elws are pacifist-vegetarian types. They wouldn't've executed Vassim no matter what he'd done. Secondly, since the Elws live through bonds (Mariel says), separation from one's family and community must be the most painful punishment they can think of. They left Mariel in Filgaia instead of Vassim because they were recently disillusioned about human violence and greed and knew that the humans would eventually be after Vassim's knowledge and skills. (To quote the short-lived King of Arctica, "Don't let them have it! They'll use it for no good!"). Besides, the humans would've forgotten that Vassim was supposed to be ostracized in a generation or so, and he could've returned to a semi-normal life. By keeping him in the Elw Dimension, they make sure his sentence is enforced.
Mystery 6: Why didn't Rudy appear to bleed after getting his arm cut off in the Gate Generator incident?
Theory: I have no #@()&ing clue. Someone please get me any logical theory in on this one!
Wild speculative theory: The Mazoku rule: OK, so this isn't Wild Arms, but it could work... The more powerful in the Mazoku hiearchy can bleed a little bit for appearances, but won't if say, their arm got blown off. Perhaps that can be applied to the Holmcross... *Thanks to Aurora Derall for this information*
Mystery 7: How did the Holmcross race die out?
Theory: The old-fashioned way, manually killing them through physical or magical means. However, the Holmcrosses are resistant to physical attacks as well as magic, which is demonstrated by Rudy (Magic couldn't heal him, so it might not be enough to actually kill him...).
Theory: The Elw created a virus or bacteria to to the job. This theory is gone into further detail in this article.
Mystery 8: If the Elw wanted all the Homlcrosses dead, why did they spare Rudy?
Theory: Temporary insanity?
Theory: They didn't. Someone took him without permission and sealed him away for some reason. This theory is explained in further detail in this article.
Mystery 9: The book "Kema" in Curan Abbey's Sealed Library says the following: "During the age of creation, one woman recieved a secret book from a heavenly messenger. The book contained information about the creation of the universe. It is said that it contains theories on alchemy and the ways of the heavens". All the books in the Sealed Library have some pertinence to the game, whether it be background info, general advice, or hints about hidden events. What is the relevence of that book?
Theory: It is background info, in the form of a Filgaian myth It could be there just to get a feel for the times before the demons.
Theory: It is background info, telling how De La Metalica came to be on Filgaia. The description of the book the woman recieved fits De La Metalica in that it is a mmagical book about things humans should not know, such as alchemy.
Theory: It's there to drive the person at the keyboard typing this up insane.
Minor Mystery 1: How the hell can berries grow in a cave?
Theory: The Guardian's power goes underground, so... it can well up in cetrain areas and cause plant life to inexplicably grow underground.
Theory: It's just a game; forget about it already!
Minor Mystery 2: Who in their right mind would give a 15-year-old boy explosives?
Theory: It's just a game; forget about it already! But still, I have this to say: Mayor Pifer, you ignorant slut.
Wild speculation 1: Were the Elw telling the truth about why the Holmcross were destroyed?
Theory: What one passes off as history isn't always true. Maybe it wasn't because they were all "killing machines", but just some went nuts and the Elw destroyed them all because of paranoia... Or maybe there are more out there somewhere...