Don't take this personally, but I would beg to differ with regards to that assessment. I have noticed a significant amount of criticism levied towards Skyward Sword on that particular basis, and I think that it is a mistake.
Granted, most games, including Zelda, are built around a simple, solid foundation. I personally think the fundamental game play of Skyward Sword is exceptionally strong. The combat, movement and item mechanics are all well integrated, and make for a rich, yet intuitive, experience.
However, Zelda was never a simple game. It as an epic adventure, and it has always strived to provide a wealth of experiences. Thus, Skyward Sword contains a number of sub-games which utilize different concepts and mechanics; the aerial sequences, the Imprisoned, and the Silent Realm all being among them.
With regards to the latter, it is certainly meant to provide a new, different kind of experience, but it also highlights the potential use of mechanics from the main title. Thus, while the Silent Realm introduces to a novel, sneak-based style of play, the game also places new focus on 'normal' mechanics such as dashing and the use of beacons.
The complete utility of these simple, often bygone mechanics could only be illustrated in this context. Similarly, the landforms of the area take on a new significance in light of the altered scenario. That's good, efficient design.
However, the Silent Realm's primary merit stems from the fact that it provides a contrast to the regular play of the game. To lose something, and then regain it, is a powerful experience. Perhaps it is less 'fun' - I don't personally think so, though it certainly is less sympathetic to the player - but doesn't it make one appreciate the main game more? That was my experience, at any rate.
Now, this not a novel concept. As I mentioned, it is typical of Zelda. Ocarina of Time featured sneaking sections and horse riding. Subsequent games have merely expanded upon these ideas, making them yet more distinct from the main game. They are, in my mind, natural consequents of the paradigmatic trends established throughout the series history.
So, while I did not particularly care for a number of the mini games (harp-playing and cart-riding...), I don't consider their existence itself to be a principal issue. Rather, I think they are very much in keeping with the spirit of the series, only now more developed than ever.
In addition, I don't think such blemishes take away from the excellence of the game in general. It is easily one of my favorite games of all time, none of which is particularly perfect. What I look for is subjective appreciation, the source of which is something different altogether.
As for being Ocarina of Time again, I think the extent of how far the developers strayed from that particular template is very impressive, and bodes well for the future. The game, I feel, carries the series spiritual legacy, as I have said, but it also knows when to forego and alter that legacy to the betterment of all.
That's just me, though.