Beyond Good and Evil was the first Nietzsche book I read - as a result, I read it without guidance and I must say not too much comprehension of what was going on. The most prominent criticisms are those of Women - I've had friends (a man, by the way, who converted from being a conservative women/gay/refugee distrusting conservative to a vegetarian feminist overnight) who could not understand how such views as are in Beyond Good and Evil to be published.
Of course, anyone who's studied Nietzsche will know how misconceived the racist/sexist perceptions are, so I won't go on too much about this.
It is hard, without having read much Nietzsche at the time, to differentiate between his sarcastic statements, his deliberate eccentricities and his sincere concerns. I think everyone at some point would like to write the way Nietzsche does - just get all your ideas out there and refuse to sensor any ideas that might seem a little askew.
What resonates in Beyond Good and Evil, as well as his distrust of organized religion and manipulative women, is his love of art. When one picks up on this value, the other statements can be interpreted toward it. e.g. what is wrong with Christianity is the suppression of the artistic soul, what is wrong with women is ... well, yes, I guess that stuff is more an expression of impotence and desire - which is indicative of a torn and longing individual, rather than a sexist one.
