Well I gotta go with what i felt was the worst of the installments and that would be, as no surprise regarding me, Skyward Sword...
Basically I felt the game fell short on a short on a number of aspects;
The overworld was definitely one of the games weak points when comparing it with others, I'll start off with the Sky. This section of the overworld is commonly criticised for what it underutilised, the Sky had potential there's no doubt about that but at the end of the day it really didn't offer all that much. Now Skyloft wasn't bad, in fact it was a rather good feature in terms of a central hub but apart from that and one or two Islands, the Sky was largely empty. Most of the Islands where small rock formations suspended in the air that housed a Goddess chest, thing is that it was no real task of enjoyment to go and obtain such treasure. Therfore 90% of the islands where just deadweight to house a chest. The Sky merely served as a hub within itself, traversing within the Sky wasn't a prolonged chore so to say but it was just so un-engaging, there was no real enjoyment from exploring the Sky, overall the Sky was the home screen which lead to portals to the surface.
Nd then this leads me onto the surface, now I have some good points and bad points about the surface over, for one it was nice that they included a lot of content, traversing the surface wasn't boring as in some other games it could be. Plus I liked how they brought dungeon aspects to the actual overworld itself. However its two strong point become weak points, having such a crammed overworld really puts less emphasis on exploration. It also gives off the feeling of claustrophobia, I felt tapped on the surface, the sections were heavily linear, I couldn't look into the distance and go and investigate, I was tapped within the confines of the rather small province. Then of course there was the factor that the surface was disconnected, essentially it was split up into three levels; Faron, Eldin and Lanayru. None where connected physically meaning that it emphasised the idea of a trapped world.
The dungeons in this game where also unfulfilling (the exception being the Lanayru Mining Facility which i loved). Each dungeon was a short experience, now I heavily express that one of the things that a dungeon should bring is a prolonged experience that draws the player. However before I was allowed to take in the experience I already reached the boss room. Each dungeon boasted a good atmosphere and we're aesthetically pleasing but they were let down in content and the experience they offered. This would be another point, diversification, now essentially in Skyward Sword we had 4 distinct themes. 4/7 in terms of unique themes is bad in my opinion, there was no real need for two dungeons to repeat the same theme and then of course the typical final dungeon which was a mixed bag like many others.
There was also the problem with exploration and how little emphasis was put on it, one thing that I think is key to any Zelda game is adventuring, games like Twilight Princess and Wind Waker executed the feeling of an adventure greatly imo. I could also mention some other things but I'll just leave what I said above, as my main reasons for why I felt it's inferior. Overall I think SS tried to make many steps forward but instead it took many steps sidewards, it didn't feel like a true Zelda game to me and putting my disappointment aside I still feel it's inferior to the other 3D titles.