Alternate Character Interpretation: Section 31 are presented in a very different light for most of the series. At this point in their history, they seem genuinely noble and more like a legitimate intelligence agency, rather than the insanely paranoid genocidal criminals of later eras.
Fan Wank: Like a lot of expanded universe stories, the novels often go to great lengths to explain away continuity errors from across the various Trek series. Taken to extremes in Tower of Babel, which attempts to weld together all the many disparate references across over 40 years of canon to planets called Rigel and aliens called Rigellians into one huge star system with numerous planets and moons inhabited by dozens of indigenous and migrant life forms, even going to far as to include background creatures from Star Trek: The Motion Picture only named in production materials.
Fanon Discontinuity: Fan dissatisfaction with "These Are The Voyages..." is made practically canon with The Good That Men Do, much to the profound relief of Enterprise fans. And Connor Trinneer, who was no happier with developments than the fanbase.
The Woobie: Malcolm Reed, who finds out in A Choice of Futures that he may never be able to have children because of accumulated damage from his years of using the transporter. He also admits to having a lot of trouble making new friends and is clearly rather upset about the splitting up of the old team as everyone gets promoted and moves on to other ships.