Most of these events have percentages calculated randomly, which means that sometimes you end up with a meaningless choice, and sometimes with a choice that can make a difference for your whole empire.
As far as the neutral choice being better than the evil choice once in a while, I think this has always happened. I always assumed it was Brad's way of inducing us to read the choices more carefully and actually think about these things rather than just Pavlonianally clicking evil (or neutral, or good) every time we see the popup.