In my opinion, Skyward sword was the worst 3D Legend of Zelda Game in the franchise. It's high points were some of the highest in the series, but those high points were few and far between.
One of the main problems I had with the game was how "idiot-proof" it felt. Nearly everything, no matter how obvious, was explained in detail, and explained multiple times. The text dragged on forever and caused common things like purchasing a set of potions to become horrible tedious. Fi was by far the worst companion in the series. I never found Navi to be that annoying, her tips were fairly concise. My experience with Fi, however, was akin to that of having someone who has previously played the game sitting next to you constantly telling you what you should be doing. Fi was especially disappointing when compared to the superb companion that was Midna in Twilight Princess.
Another problem I had with the game was the seeming lack of an overall atmosphere and it's inability to create any emotional response on my part. In previous Legend of Zelda games, specifically Majora's Mask and Twilight Princess, I was genuinely concerned about the characters and the world. I remember the feeling of dread as I waited for Kafei as the third day drew to a close, I remember feeling driven to rescue Ilia and the children of Ordon Village, and I remember the shock I felt when characters such as Mikau died, or when, after finally finding her, learned that Ilia had amnesia. These games created a very dark and mysterious atmosphere that drew me into their worlds. In comparison, I felt very detached from the world of Skyward Sword. At first, I was concerned when Zelda disappeared, but all the other characters took the situation so lightheartedly that my care about rescuing Zelda disappeared. Each of the game's locations seemed to have it's own side story or gimmick (Lost Kikwi's in Faron, buried treasure in Eldin, Timeshift stones and opening the mining facility in Lanayru), that at many occasions, I forgot exactly what my motive was. That is not to say, that all of Skyward sword's presentation was poor. The story segments taking place within the Sealed Grounds and Sealed Temple, as well as those at the end of each dungeon were some of the best in the series, however, these were also some of the only instances in which the main plot (rescuing Zelda and defeating Demise) were ever really brought up at all, causing the rest of the game to seem separated from the main story. However, I will admit that I had to play through Skyward sword again in hero mode to confirm my feelings for it as the ending of the game left me with a good taste in my mouth.
The game play is also worth noting, Skyward sword is praised for it's use of motion controls, as well as the inclusion of upgradable gear, and shield durability. These features are indeed worth of praise, but they also feel rather shallow. Upgrades were few and were also fairly cheap, by the time I had received the first portion of the Song of the Hero, I already had every possible upgrade, and over forty of most treasures. This, combined with those annoying messages you get every time you pick up a new treasure in each game play session made the system feel like a bit of a burden more so than a useful no feature. As for motion controls, I found them fine for piloting my Loftwing, or using my weapons and items, however, these were not the extent of their uses. The use of motion controls for swimming felt gimmicky and hard to control (and just made the already awful Tadtone collecting all the worse). The inclusion of things such as the tightrope walks simply added to my views on the feature as an unnecessary gimmick. I was also not that much a fan of the combat. At first, the system of swinging your sword in the direction that the enemy is not blocking was very fun, though sometimes annoying due to attacks being blocked if the sword was swung at the slightest angle. This feature of either swinging vertically of horizontally at an enemies opening, however, was basically all there was to combat for the entirety of the game, Bokoblins were the primary enemy for the entire game, and the only change ever made to their combat patterns was the change from swords to electric rods in the Lanayru province, which proved to be more frustrating than anything. In my opinion, the combat in Twilight princess was superior to that of Skyward Sword, even though Skyward sword allows you to swing your sword in many directions, Twilight princess allowed you to learn new moves such as the Helm Splitter, Back Slice, and Mortal Draw, which not only added more variety to combat, but also made it look very exciting.
My final gripe about Skyward Sword is it's overworld. The world of Skyward Sword felt more akin to a Super Mario Brothers Game than to a Legend of Zelda one. This was not due to the greater depth added to the areas, which I found to be a very interesting idea, but rather to the Linearity of the world. Skyward Sword managed to almost completely remove one of the aspects that define the Zelda series: Exploration. Every time I saw a wall that could be bombed in the world of Skyward Sword, I always got excited thinking of what may lie on the other side, as Twilight princess often featured Expansive caves or difficult puzzles on the other end of bombable walls. Skyward sword, on the other hand, would give you nothing more than a small rupee as a reward for your curiosity. To me, this was one of the game greatest failures, after completing the game, there is nothing left to do. I still play Twilight princess to this day because I find adventuring in Hyrule field and finding hidden caves, poes, or golden bugs to be a fun experience, but by the end of Skyward Sword, I had nothing left to find or do. Dowsing made finding secrets far too easy, and overall the game provided little to no post-game value.
Don't get me wrong, I still enjoyed Skyward Sword, It is just that I found it to be one of the worst games in the Legend of Zelda series, and did not find it to be the masterpiece that its predecessors were.