I don't know how gratitude crystals are a "chain quest", assuming you mean trading quest. They're nothing alike. The sidequests are all different, the quests to help people you might give a shit about, the central NPC is an interesting character, you're given multiple varying rewards, and the resolution of the quest actually affects the world in a way that only makes sense if the game has a day/night cycle. There are a few other things you can do at night off the top of my head, like trading bugs to one of Groose's henchmen or seeing another side of NPCs you normally can't, but yeah, the sidequests involving gratitude crystals are the main sidequests in the game and it's pretty weird that you apparently even think Majora's Mask's trading quest of Moon Pearl -> Town Deed -> Swamp Deed -> Mountain Deed -> Ocean Deed -> Canyon Deed is better, but whatever.
What I refer to chain quest is basically THAT 1 quest you can only do sequentially that got all the focus on development and really is about doing stuffs about unrelated npcs all over the area.
Even if that quest was trash in Majora's Mask, you have so much shit to do outside the main quest that it wouldn't affect the overall quality of the areas.
The gratitude quests are not satisfying, it's running basic errands.
The way they're structured means that they're small content you're doing between each main event of the main quest.
The worst part being that they're like 80% of the side content of the game so if they're not satisfying then side content for the game is trash.
Literally the gear upgrade is more interesting side content and way more fun to spend time with the game.
The bug trading is not even a quest , it's a protracted way to sell shit you don't need.
Your only reward is cash (and not even that much).
You can see a npc you wouldn't see otherwise? Stop the press that's something worth pointing about!
Does that npc do anything interesting?
Like you're not making a good point that there's anything worthwhile in the night of Skyloft.
They would have been better served cutting that entirely and spreading everything that's there in the rest of the game....or even add an island or 2 in the empty sky.