Were those my comments? (just curious)
If they were:
I know I sounded a little disappointed with a few things, but I wouldn't really change the essential character of the heroes.
I don't think people want flat characters, but at times they want predictability. And they want a clear "good guy" that they won't be disappointed in. If he has problems, he should be able to, in the end, get around them. (note, this is in the particular view I'm talking about, not what art should or shouldn't be). It can be jarring to see soemthing that doesn't meet these criteria, but not necessarily undesirable.
By this set of criteria, you could do what I had before: give a character two sets of desires, the "seeker of truth and justice" and something maybe a touch more selfish (though even more interesting would be something else virtuous but that might come into conflict in certain circumstances). Then have those come into conflict. If he wavers, and even chooses the more selfish motivation at times, he will be human, but still heroic if he chooses the more virtuous path when the crunch really comes.