Time for another theory rant, this time perhaps a little more intellectual-sounding than my previous "KAIN = GAYZ" one.
Shin Megami Tensei: Nocturne, henceforth referred to as Shin Megami Tensei 3, is a pretty neat game, following much of the spirit (if not even close to the brilliance) of the original two Shin Megami Tensei games as a semi-sorta-kinda-not-really sequel to them. As with SMT1 and 2, you get to choose a side between several warring factions, according to which side you believe is the better one. With SMT3, though, the lines aren't so cleanly cut between Heaven, Earth, and Hell, between Logic, Balance, and Emotion. The disciplines you have the opportunity to endorse are all more basic, human views of what the world should be, and as such, each one clearly has its elements of truth but also clearly is flawed in certain ways. And the game's fairly careful, as SMT1 and 2 were, not to show a particular bias for any path beyond the one you'd expect for choosing not to give in to any side's dogma and instead fight them all.
Save in one instance. Now, it may be small, and unimportant, and I may be reading too much into this, but there's one moment of SMT3 that sticks out to me as being, for this game, bizarrely uneven. It's like this: in the ending of the game, your main character, known semi-officially as Naoki Kashima, gets to speak with the leader of the group that he has sided with, provided he's sided with one at all, and hear that person tell him how totally awesome he is for making the world they desired come to be. Just about what you'd expect, really, right? If you sided with Chiaki, who believes in a world of eternal struggle and violent rule by the most powerful, you meet with her, and she gives you the verbal equivalent of a thumbs-up. If you sided with Hikawa, who wants a world of absolute reason and logic with no emotions or passions, he gives you the verbal equivalent of a unemotional raising of one's thumb to indicate satisfactory-but-not-emotionally-stimulating results. And if you sided with Isamu, who more or less advocates a world where everyone leaves everyone alone and has anything they want at all times so long as what they want isn't contact with any other living being in existence, his ghost will give you a verbal version of a thumbs-up that wouldn't be corporeal anyway, given his state.
To quote the bard, "One of these things is not like the others. One of these things just doesn't belong."* Yes, Isamu dies no matter what happens. Assuming that you ally with one of them, Chiaki and/or Hikawa will live to see her/his dream world's beginning, but even if it's not by your hand, Isamu's destined to go and get himself killed by Chiaki. Although, as I said, it may be nothing, it seems like an odd discrepancy.
What reason could there be, I've wondered, for singling out Isamu to die? Is it just because he, of the three discipline leaders, seems the weakest in power? I guess it could be as simple and harmless as that, but it seems odd nonetheless that they would take the time to emphasize that point. Yes, Chiaki does die if you follow her path, as well, but that's as a result of her intentionally fighting the protagonist to the death to determine which of them is the stronger and therefor the one to properly lead the way to the new world--it's the natural, acceptable result of her philosophy, a successful death, while Isamu's is against his will. And, as I said, Isamu's the only one whose death is emphasized during the ending conversation. So, as I said, it seems an odd discrepancy.
I then considered whether his death, and the idea of dying in general, could maybe just be emphasizing some part or concept of his discipline or the world he wanted to form, like Chiaki's is. But that also seemed to be a dead end. I mean, death does sort of remove you from the reach of all other people, but not in the idyllic way that Isamu wanted. And if you think of death as a way to get to Heaven or some other afterlife paradise, well, that doesn't quite work either, because those are typically thought of as places with lots of people (all the saved, chosen, virtuous, etc, depending on the version), which is definitely not what he advocated.
So it's probably not a simple show of power, and it's probably not some attempt to emphasize some aspect or virtue of his beliefs. It could just be nothing, but I couldn't very well rant about that. And anyways, I might accept most game plots not having any specific purpose in doing such a thing, but SMT games, as a general rule, have a design in every significant aspect of their story-telling. From what I've seen, at least. So I'm left with the (fairly reasonable) idea that Isamu is set apart from the others by a worse fate for a reason, something that he does or believes in that is different enough from the others that it's worthy of reprimand from the writers as being more flawed.
What I think it is, is this: Isamu's philosophy is based on inactivity, escapism, running away from reality instead of actually DOING something. Hikawa reasons out what he thinks is right and sets plans in motion to accomplish his goals, and wants to create a world of silence, logic, order. His actions and his world are about what to do, and how beings should live with each other. Chiaki, after experiencing life as a helpless wanderer in a hostile world, comes to covet the strength she lacks, comes to the conclusion that the world is and should be about the strong overcoming the weak, and sets out to gain power, and to create a world in which that is completely true. Her actions and her world are about what should be done and how beings are meant to interact with each other.
But Isamu? He isolates himself from the world in despair, and just happens across the means to change the world by fateful accident. He not only wants to run away from reality instead of dealing with it and working to change it, but he wants to create a reality that is paradoxically about rejecting itself. I mean, think about it--his world isn't one where no one else exists; it's just one where each person has his own little perfect fantasy life completely isolated from every other person having his or her own fantasy life. The reality would still be that other people existed, yet the world would be shaped in such a way to perpetuate a denial of that reality.
All three of the game's leaders have flawed visions, but Hikawa and Chiaki at least share the virtue that their disciplines are based on actually acting, working to better the world (in their eyes). Isamu just outright denies it and advocates escapism. And I think that's why he has such a notably worse fate than the others--the SMT3 creators couldn't help but subtly show his folly as worse than the others'.
* Assuming that "the bard" you're referring to is Sesame Street's songwriter.