1. Wandering Son is a pun on Wayward Son.
Wandering Son is actually a pun on Prodigal Son. The Japanese title closely resembles that for the Christian idiom. Wayward son is a good guess, for it closely resembles the idea of the prodigal son.
An important note is that prodigal son refers to the experimentation common to those going through puberty. Another note is that the other common translation of Hourou Musuko as Transient Son evokes the transsexual specific process of transitioning to the other sex.
2. Wandering Son is about traps.
The trap trope is not really present in the anime. One reason for this is that everyone knows the actual sex of the main cast. Another is that sexual orientation of main cast in the love relationships is not very clear because of the nature of puberty-related confusion. Generally a trap trope works on the conflict between heteronormity and a homosexual relationship involving a crossdresser, bishounen, or bishoujo.
3. The character designers did not make the characters distinct enough. Or, the characters look too similar.
Due to the state of the anime industry, the two-dimensional character designs – in more than one way – use crude and often sexist ways of distinguishing characters from each other. For example, one common method is to distinguish the female cast by bust size. Others include limiting the cast size and using only common archetypes, making the characters readily identifiable in any series. Wandering Son aims towards realism so foregoes such tediously common conventions.
Important Note: There is a considerable transgender audience of Wandering Son, both male-to-females and females-to-males, which one can find on youtube, tumblr, blogger, and crunchyroll. Their reactions can be very emotional and insightful.