Given you've got to have characters with strong motivations (why else are they in your story?), flaws and virtues should develop naturally out of these. Just how far will someone go to achieve their ambition? if generally they act honourably, what would make them act differently? Have you developed another character who could put them under the kind of pressure that might make them crack?
Villains need to have plausible reasons for being what they are/doing what they are doing. With very few exceptions, the vast majority of humanity has mixed motives a lot of the time for being what they are and I think fiction should reflect that. For one thing, that would add/increase tension to your story in a way that comes across as natural and not something foisted on to the plot by a writer who knows they need more tension in there somehow!