I suspect at this point that the problem with the game's hand holding is the bind Nintendo themselves got into with the Wii audience.
Simply put, if the Wii had been a bigger hit with core gamers, if it'd had a thriving ecosystem of quality, Wii-specific games like Red Steel 2, and if "hardcore" motion control epic games like Skyward Sword were taken for granted by this point... I don't think we'd see the "adventure games for dummies" packaging in Skyward Sword.
It feels as if Nintendo was deathly afraid that the remaining Wii audience is, by this point, too casual, too timid, unskilled, unmotivated, and just plain a hard sell on really getting in to a Wii game. So SS goes overboard to make sure you can't possibly get off track or confused on a myriad of points.
Sadly, judging by some reactions to the game, their fears are not entirely unfounded. Look at how many people all but refuse to learn how the motion controls really work, for instance, because it's just not worth their time at this stage to learn something they should have learned years ago had the Wii been a larger success with that audience.
Structurally and in terms of design, Skyward Sword is not a simplistic Zelda. In my opinion it's the second most complex 3D Zelda next to Twilight Princess (more complex and nuanced in some ways, less so in others.)
Its presentation just shaves off most of the sharp edges.
Personally, I am fine with this. I can overlook the foam padding. But I think it's fair that it's too much for some people.