1. The sky. It was far too empty and dull. People often say this about TP's hyrule field, but the field had a great sense of exploration and it was packed with little secrets. Some people say this about WW's great sea even though it's also full of exploration and discovery.
I don't see how The Wind Waker and Twilight Princess succeeded in these regards. Both have extremely empty overworlds in comparison to their size and scope. How much of TWW's content is actually found in the water? Barely any. That's not good, considering many of its islands were smaller than an average house. How much empty stretches of land are there in TP? A lot. That's also not good, as it has a relatively large overworld overall, even if its provinces are sectioned off by hallways. Also, how does TP provide a "great sense of exploration" when it's as linear as a hack-and-slash game? You literally can't go anywhere off the beaten path until the plot says otherwise. This is a common recurring problem in Zelda, including Skyward Sword, but it still applies to TP in every fashion.
Everything is laid out in a specific order so that the "over world" feels like a large tedious dungeon section that was put outside of a dungeon. Zelda is an adventure game not a game for completing a checklist of things in big constricted room-like areas.
That's been almost every modern Zelda, honestly. It's been "go from point A to point B" for years, and only with the release of A Link Between Worlds has it stopped being that way. And, honestly, if anything, SS was slightly less offensive about it -- emphasis on slightly. It was linear as hell, absolutely, but least its surface portions had tight level design with some sort of content around every corner, whether it be an enemy, an obstacle, a collectible, or whatever else there could be, rather than having huge chunks of empty space, and at least the objectives within them were non-linear in and of themselves. In this specific manner, SS actually hearkened back to the overworld style of A Link to the Past. It only brought it back halfway, but I'll take halfway over a continued regression.
3. The gameplay pacing. Unlike the story pacing which was even and complete, the gameplay pacing was warped. Everything took too long. Wether it be finding your bird in Skyloft, or flying to a different province, or even getting to a dungeon, everything took too long. The over world made traveling feel like a complete chore due to the linearity. Making it through an area or activity to get to a new dungeon became so discouraging that after completing the task or traversing the area, you almost felt like you didn't want to enter the dungeon because you've already done so much work to get there. This made me physically less excited to play the game again which is NOT something that a video game should do.
Speak for yourself. I was actually quite pleased with the game's pacing, aside from a few allotted moments of arbitrary padding ("Protect the Robot", Song of the Hero Quest, that kinda stuff). Pretty much every prior game just had you all but waltz up to a dungeon randomly with no real effort required to get to it. ALttP and TMC are the exceptions -- like I said, SS somewhat hearkened back to ALttP's overworld style (and in this particular case, refined it). The overworld/dungeon transition was actually smooth & natural as opposed to clunky & abrupt.
I also found a very heavy sense of progression playing through the game, as there was always some sort of new challenge being introduced, but in a very cool way. It felt like every time something new was introduced, there'd be a brief moment some time after (typically around an hour later) where it seemed like the game had either run out of ideas or was just content with sticking with what it had, but just when that feeling began to sink in, BAM, another new mechanic. I haven't played very many games with that kind of expertly-crafted pacing, and I don't think I can say that any prior Zelda game had it. Zelda's never had a single entry that became a monotonous grind of repetition throughout with low amounts of creativity, of course, but I can't describe the pacing style of any other game in the series like I just did SS's.