1. Start at the Core
The "core" is the thematic question that runs the entire length of your story. It may not be the concern of your character, but it has to be the concern of you, the author. That's why you're creating the story in the first place. You have an assumption that you want to challenge and eventually answer. After all, art is personal, so use the graphic novel to reveal the inquisitive side of you. This is what truly separates one graphic novel from another--the author's unique view of the world.
If you're doing, say, a high-adventure story involving a team, the core could be about group politics. A superhero tale could have a core involving psychological trauma in children. A romantic comedy could be really about insights on youth. Whatever the core of your story is, it should come from you and it should concern you. Because any great story tackles that human element that people can relate to.
2. Make every character a star.
Your main characters are the stars, yes, but it doesn't mean everyone else has to be cardboard. Giving your support, even peripheral, characters a nuanced presentation can enrich a reader's experience. It can be a speech pattern or a distinct look, just enough to give these characters a piece of the spotlight without necessarily hogging it away from your main characters.
Give them "business," a relatively insignificant activity that's good enough for one panel. For example, while your main characters are in their HQ talking about how to deal with a villain, show a janitor on the floor in the background working feverishly on a stain. He doesn't have to say anything, and he can only appear in one or two panels before walking away with a headache. But it's enough to show your reader that there's a "real world" that exists outside of your main characters.
3. Make your villain a mirror.
The best villains are those that totally go against what your protagonist stands for, so make sure that your villain hits a nerve. It is thesis and anti-thesis, with the hero trying to disprove the villain's convictions, and vice-versa, even if it's as fundamental as the right to live. Doing so increases the urgency for your protagonist and, in turn, increases the tension generated within the reader.
Villains need not be personified, by the way. Villains can exist in the mind of your protagonist as insecurities and past issues. Villains can be certain laws within a community. Villains can even be natural phenomena, or even a best buddy. It's not so much who or what the villain is, but the level of threat it presents to the life of your protagonist.
4. Entwine your A and B story.
The A story is your main plot. The B story is a subplot. More complex stories even have C stories. A typical action-adventure has the love angle. A typical romantic comedy segues into scenes with family and friends. A typical police thriller has a subplot about family.
Subplots are thrown in to 1) show the reader that a protagonist has other concerns outside of the main plot; 2) allow breathing space for the reader; 3) present how difficult the protagonist's situation really is by raising the stakes of the A story.
Taking off from the third item, B stories are stake-builders, and it is their most important role. It's not enough to show the reader the hero's other life, or to give the reader an occasional distraction. They would be deemed useless to the plot, and would be better off not being there in the first place. The events of the B story should eventually figure into the A story in an alarming way as you reach the climax, showing the reader that the protagonist's path to success is more complicated that originally thought.
5. Create the emotional plot.
A story plot is a series of physical events, and let's call this the physical plot. But there is another level of plot that adds greater depth to your story. The emotional plot is the journey your protagonist internally takes, which leads up to some kind of transformation at the end of your story. This is fundamentally "character development," wherein your hero begins with a specific state of mind and heart, goes through the twists and turns of your story, then ends up changed or at least, with greater insight and experience.
When you're planning the events or scenes of your characters' actions, plan as well the progression of your character's emotions. Tie that into your A and B story and you'll end up something potentially richer and more compelling.