Hello, Insert Name Here: Played with; regardless of what the PC is referred to in game, their name can still be customized (and their chosen first name can be seen in flavor text).
In-Series Nickname: In one origin, the character chooses "Hikaru Kasane" as a cover identity, and characters often refer to him/her as such. In the tech origin, the name "Subject Zero" is used, with "Zero" as a nickname.
Protagonist Without A Past: Subverted. They do have a past depending on origin chosen, but they don't find out the exact details until later. In each origin, a certain villain meddled with their lives and erased or altered their memories to conceal the deed.
At one point, however, Magi warns the player that by going out of their way to set people up with each other, while s/he may be doing the pairing a favor, s/he may be interfering with the natural course of events. Could be interpreted as a Take That against the Vocal Minority of shipping fandoms.
Verbal Judo: Can defuse a bad situation with the right dialogue options.
Everyone Loves Blondes: Generally, blonde characters who appear in the story, male (Talan, El Terre, Foremen) and female (Tala, Victoria, Bethany, Lightning) alike, have a tendency to be attractive. Vladimir is a notable exception.
Five-Man Band: One is formed by five staff members in the Global Civil War saga.