It will be find, since they're optional, they won't bother those who only play the main game.
So? Some people like to do everything in a game first playthrough. Others just rush it (speed run) and miss out on all the fun things and enjoyment in the game on their first playthrough. Having or not having optional side quests in a game wont ever change this.
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I think WW did this very well. I really felt for all of the NPCs. One of the best features of WW. But most of them were main story related.
MM sure had lots of non main story NPCs. The mask system is really what solidified it all. People like collecting things. And while earning all the masks you learnt all the back stories of all the NPCs.
SS I think was a little weak here. Apart from a few main NPCs like Groose, Granny/Impa, Zelda, Fi and the headmaster, every other NPC felt flat. You really learnt nothing about them while on the gratitude quests.
With 25GB on offer for the game, Nintendo can easily have in many side quests for items. And preferably not just gratitude crystal or skulltula collecting. As their rewards felt boring, and there's no emotional attachment to those items. The MM masks on the other hand, the item itself related to the quest you did for it. So I propose ZeldaU goes the MM route. Have the subquests/side stuff to do. But have the reward from each miniquest to relate to the people you just helped. Also you could have all the different items you earnt from the people add up to something large at the end of the game (the carrot to go out and collect them all). The carrot in MM was more heart pieces and the fierce deity mask. Not a great final reward (due to it's limited use) but much better then (at the time) useless money (cause you already bought everything) in Ocarina and SS.
In short:
Have mini stories that involve sub quests. Have the back stories of all the NPCs be told in these mini quests. Have the rewards from these mini quests directly relate to the people you just helped. Have all these rewards add up to something big near the end of the game. And lastly make this something big a worthy reward and not just more (useless at end game) rupees.