These two sum it up for my human warrior, Karis:
As a more serious answer, I really like the fear brought up in the Templar quest - that the Inquisitor would become corrupted by his power and use it to further his own ends, and basically becoming a tyrant. I think that was what my Inquisitor feared the most - power turning him into someone he doesn't want to be.
The Inquisitor's greatest fear for me?
"That he's not the Herald of Andraste."
Matched only by his other greatest fear.
"That he IS the Herald of Andraste."
She's a devout-but-increasingly-progressive Andrastian who wants to believe in Andraste's and the Maker's favor because the world desperately needs hope and so does she, but at the same time she fears it's the worst sort of blasphemous hubris. Add a touch of "How can anyone live up to THAT?" combined with general fear of the heavy consequences of failure (hello, end of the world as we know it), and you have a person who wrestles with faith a lot. Fun to roleplay, as a real-world atheist.
The dangers of corruption -- for one reason of another -- are constantly thrown in our face. Blind obedience, despair, lust for power, deluding yourself that you're acting for "the people" or "freedom" or "the greater good" ... so many ways to lose one's path, as have many other organizations and people. It's definitely a theme that any Inquisitor should strongly keep in mind. Karis is afraid of going down that path -- and if she doesn't, who says whoever picks up her legacy won't?