Expy: The administrator in Ge'en, Sister Alessandra, is seen as one for Josef Mengele.
Lying Creator: Despite promises that a stealth mechanic wouldn't be present in the game, due to the criticism it received in Dreamfall, stealth sections do appear in Books 2 and 4, though they are a lot simpler and more forgiving compared to the ones in Dreamfall. It is even Lampshaded, as getting discovered unlocks an achievement named "I thought there wouldn't be stealth!"
The Other Darrin: Many actors were replaced, barring a few. Most characters from The Longest Journey keep their original voices. Zoe's change in voice is handwaved as being an after affect from spending so much time in a coma.
Word of Gay: The developers had to confirm Kian was gay in a forum post after some dialogue with Enu brought up the question.