I knew when I saw this that it would turn into yet another opportunity for everybody to bash Skyward Sword.
I liked that game so I'm gonna leave it.
On the subject of story plots, FS and MC have the worst plots in the whole wide world.
But to be honest, the most annoying element of story-telling for me within Zelda is probably simply the way Link just meets random people and does what they tell him to. OoT is probably the worst offender of these in my opinion, despite the fact it's my favourite game and it's plot is almost flawless... However, I don't really understand why he listens to some people or why he even trusts them. Aside from the Great Deku Tree, who is pretty much Link's father figure and thus it makes sense...
1) Zelda is basically just a kid like Link. I know the Deku Tree says to go to her, but why would Link really go and risk his life for some little girl who had some funky dreams? So what if she's a princess? I live in England but if Princess Beatrice or someone told me to go and put my neck on the line for a couple of stones because she doesn't want to listen to what her dad tells her (that Ganondorf is trustworthy) I wouldn't do it
2) Sheik. He/she (I'm not here to debate this particular point) just randomly appears. Literally, appears. He/she says some random poetic sounding lines, and Link just listens to what Sheik says. I don't see why, pre-Ice Cavern, when Sheik saves Ruto, Link would assume Sheik is good and should be listened to
3) Any Sage other than Saria. Saria is Link's best friend so it's kind of a duh that he would go and save her and listen to her advice. However, Darunia is pretty rude to Link yet Link goes and fights a giant firebreathing lizard type thing for him and his people. Ruto is a cow, demanding to be carried everywhere and getting herself swallowed- oh and she then basically decides for you that you are going to marry her and you don't get a say in it. U ok Link? Impa... I mean, I love Impa, but again there is no real evidence until you go to the village and hear people talk about her that she is this nice person who should be trusted. But Link takes her word before you chronologically go to Kakariko that Zelda should be believed. Last but definitely not least, Nabooru. She tells him to go and steal stuff for her. I know she says she's against Ganondorf but Link sees no proof of this, and even if he did, no normal person would just do what she said.
4) Okay it's possible Link is just nice, but to me he seems like a pushover.
So yeah, I think the story has a little to be desired in this area.