The reveal that Merle was a Zoroark all along made many a reader take a second look at all the hints given along the way to show that they all made sense.
The Alola Trilogy pretty much seems to just be an adventure in the style of the anime with some of the series' other hallmarks...until about halfway through one realizes that the entire trilogy is really the characters dealing with the PTSD that the Kalos Trilogy inflicted on them.
The Pikashunium-Z showing off Ho-oh's colors and Ash connecting his dream to the day he saw Ho-oh, allowing it to manifest. It's later used by Ash as proof of needing to earn Ho-oh's power.
