Calling Skyward Sword the "Best Zelda game" is an overstatement because it failed to improve on the shortcomings of its predecessors and failed to deliver on some of its major promises.
The lack of variety in environments was a major turn-off for me. Considering the scope of past game worlds, especially Twilight Princess' Hyrule, being limited to forest, volcano, and desert regions as well as a standard hub felt very constricting. Although Nintendo managed to make each area feel unique by offering unique challenges which succeeded in maintaining some level of excitement upon return visits, some of these designs could have been used in new regions to further enhance each geographic region. For example, many fans have remarked that Skyward Sword should have included an ice region. This would have been a logical fit for the boat sequence in Lanayru and provided more diversity for the Timeshift Stones, a revitalizing yet underused mechanic for the now commonplace time manipulation found in Zelda games.
There were a lot of external factors affecting Skyward Sword's reception too. It had been five years since the release of the last console game, Twilight Princess, and the Wii had no AAA games other than Skyward Sword. Also, with the developers hyping Skyward Sword to be the next leap for the franchise, seemingly minor issues were harped upon by the community. Skyward Sword's motion controls are the most precise the industry has seen to date, but the attention is always towards what wasn't delivered pointing out the motion aren't 1:1 after all even if they come close.
I know the Ocarina of Time talk gets old, yet it was a big deal back then because it did so much right and turned the industry on its head. It was the most ambitious game of the year even amongst the likes of games like the original Half-Life and Metal Gear Solid. Ocarina pushed the N64's graphics more than any game then besides Banjo Kazooie and offered its greatest contribution in the now standard targeting feature found in many shooter games. It was also a straight up fun to play game with hardly any filler compared to the games of today.
Although Skyward Sword was a phenomenal title, it didn't do enough to distinguish itself from 2011's other major hitters, especially the adventure game that did soak up the most acclaim that year, Skyrim. Aonuma realizes that the franchise has played off Ocarina of Time's success for too long and is trying to redefine the series. That change will come eventually, but we're not there yet. Skyward Sword and A Link Between Worlds are transition titles, adding in several new gameplay mechanics and stretching back to deep series roots, while the true Zelda reboot lies in progress taking note of the successes of the failures of its predecessors and the gaming scene at large.