At first blush, Yu-Gi-Oh!'s take on Egyptian mythology (and history) seems about as accurate as ducks giving out candy eggs on Halloween. And it would be stupid to deny that some extreme artistic liberties were taken. But with a closer look (and some research), one starts to realize that, maybe, just maybe, Takahashi did the research, and maybe, just maybe, he actually cared about the mythology when he wrote the series (even if there never were any Lovecraftian kaiju being worshiped as gods-- Zorc was supposed to be a secret, anyhow, so you have to forgive that.)
I'll start with Kul Elna, because after that I'll be trotting right out of historical accuracies and headlong into the messy world of Egyptian mythology, which is a pretty scary place.
Understanding Egyptian culture makes everything about Kul Elna suddenly fall into place much more clearly: the reason Aknadin was so certain everyone there was scum, the reason he knew where it was, and the reason the main person who felt guilt over Kul Elna was Atem's father, a much more compassionate man than Aknadin could ever claim to be.
In ancient Egypt, there was a such thing as villages of exile. While my sources generally agree that the people sent there usually had their noses cut off first, we can forgive the presence of noses on Kul Elna's citizens for the simple fact that noselessness is really nasty to try to draw. Criminals were sent to these villages, usually on the outskirts of civilized society, for crimes ranging from thievery to assault (murderers were usually executed quickly.) They were unallowed to have marriage contracts and other kinds of contracts, but that wouldn't have stopped them from having children or eking out their lives. Shunned from society, these people could easily decide that perhaps, they weren't really a part of their country anymore, which is why Thief King Bakura would have held the country and the royalty in such high contempt.
So why did Aknadin know that everyone in Kul Elna was a criminal? Because he'd probably sent a lot of them there himself. Kul Elna was a village of the exiled.
Moving on to kas, bas and souls. In Yu-Gi-Oh!, of course, a ka is a monster connected to one person, who maybe can summon that monster or who may lose said creature when it gets sealed into a tablet. Kisara's ka was stated as also being her ba, which was why losing her ka would kill her.
Now, the cliff notes version of the actual mythology is essentially this: The ba is the soul that leaves the body at death, the ka hangs around and lives in the body after death. That doesn't sound anything at all like the Yu-Gi-Oh kas, of course, although in Yu-Gi-Oh the ba WAS treated as a life force, so that's okay.
But the kas, despite having obvious liberties taken, are actually much closer to the original mythology than you might think. According to the Book of the Dead (Coming Forth By Day), the ka and ba were both fashioned before birth, and while the ba lived in the physical world, the ka lived in a mirror spirit world, changing and growing alongside the person it belonged to.
So actually, it makes perfect sense that a person's ka would reflect their soul's state of being before death. The manga implies strongly that everyone has a ka, it's just that only some people are magically powerful or talented enough to bring their ka into the physical world. The most probable answer as to why people aren't always summoning ka in Yu-Gi-Oh's modern setting is simply that "the brave pharaoh locked the magic away--" running around in the real world isn't the natural state of a ka, so it can only happen a lot when there's a lot of free-floating magic.
The ka and ba were regarded as two parts to one spiritual body, another part of which, the akh,(described elsewhere as "a combination of the ba and ka," although not in the books I was reading, only online) is considered to be closer to the modern concept of a soul-- not a life force, not a mirror world twin, but rather the "thing" that makes us who we are. Most likely, the part of the soul that both Pegasus and Yami Bakura were given to sealing into cards and game pieces was the akh, and it was probably Atem's and Bakura's akhs that were sealed into the Puzzle and Ring. The ba was fragile, the ka removable and removed from the body during life, but the akh was nigh indestructable.
This is part of why I regard modern Seto Kaiba as being the soul-offspring of Priest Seto and Kisara, by the way-- his ka is most probably a Blue Eyes, and his ka is part of his spiritual body, not a separate thing that follows him around. Whether it was the akh, some fragment of ba, or some other spiritual organ besides that he inherited from Priest Seto, only Takahashi can answer (and to be frank, I'd rather he not, so don't any of you dare ask him.)
Within Yu-Gi-Oh, of course, one assumes that the ka is rather like a spiritual kidney-- you can live without the whole thing, but that doesn't mean you'd want to. It's shown that separation from the ka is mind-numbingly painful. Further, Thief King Bakura's ka, Diabound, changes through his part in the story, from pure in his quest for justice, to tainted and dark as Zorc begins to twist him. Something else that isn't ever stated explicitly in the dub but seems pretty clear in the manga is that people can use the powers that belong to their own ka. Bakura was doing it all the time, showing up where he shouldn't, blasting people when Diabound was nowhere to be seen, getting into places that were supposedly death traps. If that isn't a good argument that the ka is a part of a person, not something that follows a person around, I don't know what would be.
All things considered, a little research into what kas and bas actually were in the original mythology helps Yu-Gi-Oh to make a lot more sense, like, for example, why a soulless body becomes insensate and zombielike instead of simply dying (the ba or life force is still there, it's just the akh or will and personality that's been taken away.) Which is another reason why doing the research is good for fanfiction. (Glares in the fandom's general directon.)
This does beg the question of what exactly was going on with regards to the Oriechalcos. (If you discount the idea that the writers of that arc didn't know about the multiple soul concept.) Obviously, the ba remained in the body, since the bodies became comatose instead of dying. But then how were the souls being used to power the Leviathan, if they were akhs and not bas? They couldn't have been using the akhs to draw on the bas, because a lot of the people Dartz victimized had died a long time ago, their bas leaving with their deaths.
We pondered this question together for a few moments, but it didn't take Invid very long to suggest an answer: The akhs are tied to the kas-- and the Leviathan was feeding off the kas and akhs together. This was why there were a multitude of Duel Monsters, and why the Duel Monster world was in such turmoil and dire danger: it is the world that kas live in, and Duel Monsters are kas. At the time of Atlantis, there would have been a lot of free-floating, positive magic surrounding Atlantis itself, which would have been why you'd see fairies and the like wandering around. When the Oriechalcos arrived, it began twisting that magic, and what happened to people like Dartz's wife could be interpreted as her darkening ka twisting and taking over her body.
I'm going to take a moment to put forth a theory I've had about GX for some time, and since I almost never discuss GX (and don't count it or 5Ds in YnY's canon) you might as well listen up: I strongly suspect that Judai was originally a ka. That is, the weird kingdom that he and Yubel originally hailed from, wherein he was a prince, was actually within the ka-world seen during the Oriechalcos arc, which is why it doesn't resemble anything within real history at all. Whether this has anything to do with his strong sensitivity to spirit creatures (Hey, Rafael could talk to them too, so I'm not complaining about his or Luna's ability to do so) or with Yubel's.... Yubelness, who knows?
Please note; I do not claim to be a professional egyptologist. This essay merely desires to use what I know about the actual mythology, and backtrack what Kazuki Takahashi did with it to see how it might apply to Yu-Gi-Oh! Certain descriptions, including that of the akh, are rather confused in the original mythology, but mainly because they had several millenia to think about the subject. I might have considered labeling that aspect of "soul" the "ib," which Wikipedia does agree was the seat of emotion, but the ib was also the physical heart, and it's rather obvious that Pegasus wasn't ripping people's hearts out. :x There were two other parts of the soul, the "sheut," or shadow, and the "ren," or name. (And since it was considered part of his soul, you can understand why it was so key for Atem to get his name back.)
(Which implies that it's possible that a soulless shell in YGO, despite divested of willpower, might still have faint emotional response to things going on around it. So it's just as well that Kaiba said "no" to dueling Mokuba.)