Collecting things has been a time honored method behind not only every Zelda game so far, but most fantasy games in general. There are normally something special and magical like keys, crystal shards, or some other magical plot inducing maguffin that the hero requires to save the kingdom or gain entry into the villain's castle. In fact this method of storytelling is a little bit older than the video game series that repeat it. It is common in fantasy storytelling in general. So I really see no problem with the concept since collecting items is another aspect of the exploration based gameplay that Zelda is so well known for. Even between dungeons it gives the player something else to do and accomplish. The series had had a large number of non collecting sidequests in the past, MM is a great example of that. It may jsut be that we have not seen any yet because various sources giving away previews have not focused on the story nearly as much as the gameplay. It is much easier to show off the features of a game in a two minute video displaying a quick item collecting and upgrade sequence than it is to show story. Even then there are more people who would consider it spoilers and not wish to see it before the game is released. So I would not expect to see as much at this point in time at all.
Also for a storytelling purpose, I believe Link in SS has a little bit more of a motivation than many of the Link's in past games. Link in LoZ only saved Hyrule because his sense of justice told him it was the right thing to do. That and he really had nothing else to do that day. In AoL he mostly wanted to get this strange triforce tattoo off his hand, and btw there is also a princess that has been cursed to sleep for a few centuries so it would be nice to save her while he was out. ALTTP Link rescued Zelda in the first mission, he really had no need to get himself involved in stopping Aganihm or going to the Dark World and making things right. It seemed to be more of a see things through to the end kind of situation. OoT Link had nightmares and left on his quest because it was a dying wish of the Deku Tree. In MM Link wanted his horse back and the Deku Mask taken off. The mask was removed within the first few minutes of gameplay but that still did not stop him from roaming all around Termina helping everyone he could while repeating the same three days over and over again.
The way things are looking now, it seems that Fi might be pushing Link towards not just saving Zelda, but the entire land below. Much like Link of WW only wanted to save his sister but the KoRL came along and took him on a quest to save all of Hyrule. The Link of TP only wished to rescue Ilia and the children but Midna had him agree to help her save her kingdom and stop Zant. Link in recent games is more manipulated into the greater quest by various NPCs, but it is still the right thing to do so we never really see him actually get annoyed or angry about it. He is still the hero after all, it would be more terrible if he did give up and go home if his personal interest in the quest was fulfilled. Even then, in most games Link is generally some kind of outsider that discovers the lands and people at the same time as the player. We slowly learn about the plight of the people that are under attack and become absorbed into the greater picture. ALTTP Link learns of the people suffering under Ganon in the Dark World, OoT Link sees the destruction caused by Ganondorf, WW Link learns of the actual fate of Hyrule and TP Link see's what Zant is doing to the people in the Light World first hand. He could not possibly quit after getting started in his quest becuase these threats are too big and would eventually engulf other people in other countries if they are not stopped now. We have already been told that Link of SS knows nothing of the world below. It might be a similar situation as Link discovering the Dark World, or seeing Hyrule covered in Twilight, he sees that the land below is suffering under some cruel villain and genuinely wishes to do something about it. Apart from just saving Zelda and returning home, that might be the motivation behind the first couple dungeons before he really learns the true story of the land below and why people are living in Skyloft today.
