I would've liked to see the Hidden Skills appear, and maybe then some, but in many ways I think that Skyward Sword was a test run. It introduced a lot of fresh attributes to this series (upgrading weapons, the Goddess Cubes, etc.), and even brought others back (the Sword Beam, and Tear-collecting to name a couple). Skyward Sword worked prodigiously to improve upon the foundation of the Zelda formula.
The motion controls themselves give off loads of movement-based combat, and with very little button mashing. No other Link before this release was able to perform a Spin Attack upwards or downwards. But they were limited enough as to lot allow the player to gain a complete advantage over enemies. If the Hidden Skills were brought into the mix, things would have been a whole lot easier. For one thing Skyward Sword's enemies had to be amongst the most standard or else we'd certainly see more of the harder kinds, such as Darknuts. Overall SS was rather effortless, at least to me, because it seemed more like a first stab at motion-oriented gameplay rather than full-fledged engagement. I think that's what Nintendo was aiming for, more than anything.
Again the Hidden Skills would have lightened this game on far too many levels. Had they been implemented in more situations than a battle--like for puzzles--they would've been more applicable to a game of this caliber. I'm not calling SS child's play, but many people had to adjust to the new controls; this is something that Nintendo foresaw as necessary, and they decided to help new fans become immersed in the game firstly. Providing shortcuts such as the Skills wouldn't really offer them a wholesome experience, but they also balanced the level of difficulty out where it wouldn't overbear them.
So I can understand they the Hidden Skills were left out from this game. But I hope to see them reinstated in the next one.