The problem for me wasnt complex shades of grey in the characters motivations, just arbitrary jumps from one thing to another - Holt is happy to shoot Spore, but gets all upset when they shoot Run... Buchanan is alternately bleeding heart liberal and alienist murderer. This isnt to say characters have to fit "good" and "bad" roles, just that their motivations need to seem logical and -erm- motivated by their experiences, rather than the needs of the plot.
In the end, is the message that we'll all end up taking sides when push comes to shove, and the lines of race are as good as any to take? Does the ending sees Holt throw his lot in with the aliens, because he is one himself, or because their cause is the right one? By throwing your lot in, does that mean adopting the extreme methods of Spore and Run? Is this actually a good thing, because it's only extreme pressure thats lead the aliens to these actions, so they are justified, or are you perpetuating a cycle of violence? There's a lot of interesting issues raised there, but I'm not really sure the strip even scratches the surface of any of them. Even when it does touch on these issues, it just seemed heavy handed and unconvincing IMO.