This is only a very small thing but I have noticed that when you are given a yes/no choice it is sometimes set up so "Yes" is above "No" and on other occasions "No" is above "Yes", it would be nice to have it constant.

In my opinion it should always be:
[Yes]
[No]
[Any other selection]

I think yes should be on top because usually when you get a Yes/No selection most of the time you got to that selection because you wanted to say Yes. (and of course if you are just bashing enter and accidently click yes you deserved it for not reading the awesome dialogue in this game)