>>38490686I assume OP is referring to the one relating to Shiny hunting, although if we're talking about Masuda's approach to story at least from what we see in Gens 3-6, the one's he directed, they all tend to focus on the idea of a sealed Legendary Pokemon being awakened in some way by the villainous team with varying degrees of success in the villains goals. RS had Maxie & Archie achieve their goals although had the decent realization that unleashing a Pokemon known for scorching the land or a Pokemon known for controlling the ocean would wreak havoc. DP had Cyrus almost succeed although he couldn't really do anything since the player bests him, outside of the distortion of Sinnoh which seems to have no lasting impact, it's kind of a missed opportunity that Dialga & Palkia don't cause some weird shit to happen.
BW is perhaps the unique one of the four since the legendaries aren't beings of magic and more so are beings of might. Reshiram & Zekrom are just sort of really powerful dragons so N achieving his goal of obtaining one of them is understandable in that it doesn't have an immediate impact on the region although at the same time it's never clear how getting the dragon would allow N to force people to release their Pokemon, nothing in Reshiram or Zekrom's abilities suggest they can somehow control Pokemon and Zekrom can get bodied pretty hard by an Ice Cream. XY is the closest to RS in terms of its plot although at the same time is trying to be Team Rocket, think about it, first proper encounter is in a cave, hideout is located in a big city, battle the big bad three times before they disappear. Xerneas & Yveltal are also a return to the Dialga & Palkia situation, they do fuck all in terms of their abilities, yeah they're being used as an energy source but we'd see Xerneas cause Grass & Fairy Type Pokemon to randomly start appearing all over the place while Yveltal would cause Ghost Type Pokemon to randomly start appearing (obviously they won't show death).