One of the biggest factors that many creators fail to acknowledge is the lack of fan base to drive their comics forward. There are many reasons for this outcome but the most common are these:

Somewhere along the lines you got a little to busy with the awesome battle that you might have forgotten to show your readers why they should care. Even more did you even evaluate the reason, did it sound concerning or believable, how about interesting? Your story has no roots!
Build this up by creating tension between heroes and villains. Add real problems. Make the hard choices. Build a history with your characters so that your readers feel like they have a stake in it.

The damsel in distress doesn't work in a world fighting for equal rights for men and women. You'll end up with a mediocre response. Avengers: Civil War is practically about human rights. X-Men: Age of Apocalypse is about choosing sides on morality and so on. Find a topic to parallel and work you major conflict from there. A lot of these topics will involve what's wrong or right scenarios and does the end justify the means type questions.
Remember to build your fan base up before releasing a major conflict title. You can use a series of stories leading up to the major issue. This will help get that major title off the ground when you release it since the issues leading up to it will act as your marketing and advertising.