Getting the main story of a game right is incredibly difficult. Being able to correctly pace reveals and narrative highs, weaving in gameplay and remaining interesting throughout is a delicate balancing act - one that a lot of games slip up on. You often get belaboured portions of wasted time, or parts that speed by with monotonous questing.
All of which is why you see more and more people touting different side-quests as being the best parts of games, especially open-world titles. Many side-quests are small, self-contained stories that allow the creative minds behind the game an opportunity to throw aside the shackles of the main story and do some really interesting stuff.
There is no pressure for a grandiose story or climax, so you have these tight-knit experiences that sometimes feel more memorable than the main game.
It is a constant trend throughout games that side-quests often have that degree of polish. And with the current zeitgeist being bigger and bigger games, the next few years are undoubtedly going to spew out many more titles where the smaller, less bombastic quests are actually the most enjoyable part.