There is a third option as well as good human/evil alien and evil human/good alien approach: the Warhammer 40k approach: present everyone as self-interested bastards willing to do whatever it takes to further their own aims.
No matter which side you look at it from, there are no 'good-guys' in the traditional sense, which to me makes it considerably more interesting:
The Imperium of Man in 40k could certainly be construed as the 'hero', simply because the great majority of fiction and fluff is written from their viewpoint and the fact that they're human makes them easier to empathise with. However, when you actually step back and look at the Imperium, it is a vicious, xenophobic, repressive regime capable of committing atrocities that seem far more in the vein of various historical dictators (this is something I feel we should tell all the 12 year olds playing Space Marines because they are 'teh go0d guiz'...)
Then, having looked at the Imperium from our perspective, looking at it from the perspective of the Imperium itself, much of what they do can be seen as reasonable and necessary: when you consider the threats faced by the Imperium from all sides by foes with no grasp of the idea of mercy, the xenophobia and brutality of the regime becomes a necessity for the survival of humanity.
The same holds true for the other races that could be viewed as 'good':
Eldar: Arrogant, cruel and utterly self-interested. Whilst they share a common enemy with the Imperium in the forces of Chaos, they are only interested in their survival and don't care how many humans have to die to save an Eldar life.
Tau: Space Communists. 'Nuff said really....
I personally find this lack of any ideological 'good' quite refreshing, and I think it's something that hasn't really been made enough of in the Dawn of War games, where, with the possible exception of the Eldar in places, very little has been made of the utterly pragmatic self-interest that defines all the factions, especially the pseudo-religious zealotry of the Space Marines, who seem to be portrayed in an almost exclusively positive light.
Anyway, I suppose the whole point of this thoroughly long winded post (Im procrastinating...) is to agree with the OP and say that I think that any game that challenges the normal perceptions of good and evil in games would be a very positive development.
edit:
Jamash said:
Warhammer 40K: Fire Warrior is a bit like that.
In that game you control a heroic alien (Fire Warrior) fighting against the 'evil', oppressive 'Imperium of Man'.
Although it can be argued that the Tau are hardly saints (but then, who is in the 40K universe?), even though they're fighting for the "Greater Good", but that's more in the fluff of WH40K and not really in the context of the game.
Ahh, don't know much about Fire Warrior, hence why I haven't talked about it above, but you make a good point.
On the subject of the Greater Good: for the Tau the Greater Good is the greater good of the Tau 'Empire' (never understood why they're calling it an empire now...): the ethereals don't care what it takes to work towards the greater good, or indeed what sacrifices are necessary. I believe that there is fluff of Tau colonists slaughtering the inhabitants of conquered Imperial worlds that refused to accept the Greater Good.
