Let me start by giving credit where it's due. The line of thought explored here grew from a discussion on the [url=http://carnage.bungie.org/haloforum/halo.forum.pl?read=858222]HBO forum[/url], which was itself inspired by a [url=http://jparish.1up.com/do/blogEntry?bId=8551185&publicUserId=5379721]tho... article[/url] from 1UP's Jeremy Parish.
My own contribution to the HBO discussion was to speculate that unfavourable reactions from many fans to the Arbiter levels in Halo 2 led to Bungie scaling back the Arbiter's role in Halo 3, tending to impoverish the story. Anyone who followed community discussion after Halo 2's release will probably remember many comments from those who were uninterested in or emphatically hostile to the idea of putting themselves in the Arbiter's - er - hooves.
To those of us who were willing and able to make the effort, and found it rewarding, this widespread failure of empathy has many disturbing implications. The one which concerns me here is the potential effect on Bungie's future decisions regarding storytelling technique, and the level of moral complexity fans are willing to deal with. As an unashamed, card-carrying member of the 'cerebral' wing of Bungie's fan community, my personal preference should be obvious, and I'm certainly not the only one who's worried about this.
My thesis is that many of those hostile to the Arbiter aren't inherently hostile to complexity, moral or otherwise. Their problem may be more to do with the situation and expectations set up by Halo CE. If it had been clear from the start that we were going to see the war from both sides, then maybe they wouldn't have reacted so badly when they found themselves in the Arbiter's skin. That's not a criticism of those who put the story together - I'm speaking here with the advantage of hindsight. The level of emotional commitment to the cause of Earth and the UNSC displayed by many of these fans is impressive, as well as more than a little frightening, and may in part be due to the real-world events of the period.
As an aside, I've often wondered if the character of the Grunts was intended in part as the thin end of the wedge to prepare us to empathise with the Covenant species. Grunts are hard to hate, and they have many explicitly childlike characteristics - their size, emotional volatility and high-pitched voices, for example. Call me a sentimental fool if you like, but in Halo 2, when infiltrating the Delta Halo Shield Wall as the Arbiter and picking up stranded Grunts and Jackals on the way, I sometimes couldn't help feeling like a harried mother herding cute, easily-distracted toddlers through a bad part of town.
I sincerely hope I haven't spoiled anyone's enjoyment with this speculation, but if the vague possibility that you've been gleefully shooting and clubbing child-surrogate figures to death for years doesn't cause you the slightest twinge of uneasiness, then there's something badly wrong with you, in my opinion. The game requires you to kill them, but hating them is another matter.
If this admittedly macabre theory is on target, why was this device not more successful in generating a willingness to empathise? I think it's possible that the Grunts' comedic value may have undercut their other attributes - players were too busy laughing at them to take them seriously or find them sympathetic. On the other hand, that humour is an integral part of Halo, and the game wouldn't have been the same without it.
Back on my central topic, there definitely is a sizeable audience for fiction which goes beyond black-and-white comic-book morality (though that's actually rather unfair to the modern comic-book genre), Two examples with substantial crossover to the Halo community spring to mind; the first is BioShock, and the second, and perhaps more directly relevant, is Ron Moore's re-imagined Battlestar Galactica.
In conclusion, I must acknowledge the enormous risks Bungie, or any other modern game developer, run in putting together a game design and committing to a project. The running costs of a modern studio with over a hundred staff are frankly terrifying to contemplate, and the investment of human lifespan, blood, sweat and tears involved in a multi-year project implies a heavy moral obligation to ensure that these precious resources are not wasted. I don't expect them to make timid, easy or obvious choices, since that's not what they're about. I just hope that they don't have to sacrifice too much of their soul in order to survive and prosper.