As for legendary Pokémon being "MacGuffins", I agree that Ho-Oh/Lugia in HG/SS and Xerneas/Yveltal in X/Y are the only real examples of this. They were both just forced into the story for no real good reason. While I like X/Y on the whole as well as their legendaries, I do think the story/characters/lore is one of their weakest parts. Which also makes me wonder what it could have been like in a follow-up game... I guess we'll never know.
I'd argue against Ho-oh and Lugia being MacGuffins in HGSS. One of the central themes in those games is about Pokemon trusting humans; this is expressed clearly through the test in the Dragon's Den Shrine, the player defeating Team Rocket, and the fact that Pokemon in HGSS walk with the player, among other things. It's referenced explicitly in the plot with the people of Ecruteak driving the legendary beasts away out of fear, and the player subsequently getting close to Suicune. The Kimono Girls observe the player becoming a powerful, compassionate Trainer who can connect with Pokemon, and this is what causes the box legendary to appear before them. It's not for no reason, either: it's made clear that bringing the box legend back will be a good omen for the bonds between people and Pokemon.
I actually think it was a fairly refreshing, and subtly mature way to incorporate the legends into the plot, compared to the doomsday scenarios seen in other games.
X and Y, though... dreadful. I despise those games, not least because they came so close to being really great. There's so much that's almost great about them, but they miss the mark on almost every count.
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