Something to really watch out for is taking on an anti-religious/anti-military theme. This isn't because of some need to avoid controversy or to avoid fanatics of either flavor. It's because you can't always pull this one off.
The inherent attraction with both themes are that they are large organizations with an inherent organization, and with a history of doing bad things. This is definitely antithetical to the artist, who must rebel against authority and seeks to do good.
It must be realized that they are organizations, not individuals. Both organizations have done a lot of good, especially for the arts. The various armed forces have defended the same freedoms that they stand accused of destroying. They have helped those in emergencies, given people a way to change their lives, and given confidence to those that didn't have it.
Unfortunately, too many people see the violence and that the military needs to have a different set of rules in order to function. They also see a lot of crimes that tend to not happen, or at least not as bad as the conspiracy theorists would have you believe. This isn't to say that the military doesn't commit crimes. It does. But you need to realize that there is a huge difference between a soldier raping someone and that being sanctioned (it never is).
Dealing with an alien species is always difficult, especially if you don't like that species. Artists have always likened the military to ants; following orders no matter what, even if it means its doom. How can humans follow orders that could mean their deaths? It's difficult to understand, but that loyalty, with the understanding that your life may be save hundreds of others, makes the action have sense.
If you could save thousands of people, would you? Are you willing to draw a line in the sand, and then back it up? If someone was going to do their level best to destroy your country, including destroying all that you holdd dear, would you fight for it or run? Either choice is legitimate; running and setting up elsewhere is an acceptable decision. However, it needs to be realized that taking a stand is just as legitimate a decision. Pacificism is more extreme than violence is; one willing to defend is willing to defend all, but a pacificist will attack those defending him...
The various organized religions may have committed crimes throughout the ages, but they have also done a lot of good. The same church that burned witches also found a way for girls made pregnant to escape their families. They also ofered what succor they could during disease, famine, and war. In times of war, they were the ones to barter for peace; boxing was the creation of a priest wanting to find a way to stop nobles from fighting to the death. Religious men have led the fight for civil rights, or was it forgotten that Ghandi and MLK, Jr., were a priest and a reverend respectively?
The various religions may have flaws, but they weren't without their share of merits as well.
And both have done their fair share for art, as well. Religion has inspired and commissioned some of the greatest masterpieces in the world, and that military's need for records has also shown to be a springboard for art, especially in those who job it was to go along with the soldiers. Just something to consider when you are about to do yet another "it sucks to be in the military" and "the church should go away" story...Does the benefits of the organization outweigh the issues, or do the issues outweigh the benefits?