Important questions to ask yourself after you've got your basic story, but before you start to work out the panel by panel details.
Here it is:
What is the story's (a) Dominant MICE quotient?
(b) Primary Conflict?
(d) Major World rules and limitations?
I'll use Miazaki's film Nausicaa as an example:
(a) Idea: Man versus nature - Man's place in nature. Why do humans often come into conflict with nature and what are the solutions to overcome this?
(b) Fear: Fear of the unknown, fear for one's own survival, and the consequences associated with acting out in fear.
(c) Love: The only way to overcome the obstacles in life is to act out of love. You destroy your enemies by turning them into your friends, and you begin to understand the mysteries surrounded about you by thinking/acting on behalf of those around you before you act for yourself.
(d) Giant insects/spreading toxic forrest = man is not the dominant species on the planet, our lives become more fragile. Warring nations = freedom to choose way of life can be restricted. Ancient technology is unearthed = a few people can gain control over many, pushes an oligarchical system of rule.
You might see a loose connection here. Pointing out your (a) story emphasis will lead to questions like (b) why it is and (c) how is it solved? And then we have to think of the (d) method of execution in telling our story. This connection may or may not be there, but it's certainly important to investigate.