[...] Anyway I sincerely hope that Inquisition fixes this problem and makes more branching choices. It isn't always A or B there is usually a C.
Agreed. The question of "what is morality" or "what is morally right" is certainly not so easy to answer. Maybe that's why video games tend to simplify matters. It would be a welcome step if DAI shows the whole range of possibilities, so, as you said, A, B and C.
Speaking of grey, I thought The Witcher did a very nice job of portraying it. No matter whose side you chose, your choice was never entirely good or bad. That's what I liked about it. I like choices were the player is forced to think about it. That being said, I probably prefer a non-visible system were you can shape your character's morality through his actions and their consequences.
In addition, this thread inspired me to do a little bit of research about morality in videogames. I came across this article. It mentions Mass Effect, so I thought some of you might find it interesting.