They are dumbing Zelda down in many ways.
Skyward Sword have some great things going for it. The "travel > go to dungeon > get item in dungeon > use item to get to new area" formula has been shaken up quite a bit, I really liked the more natural progression in the game world, with some backtracking that most of the time didnt make the game feel stale. The dungeons were also shrunken quite a bit, which I liked, I always had more fun exploring the overworld than the dungeons (goes for every zelda game).
Most negative things (brought up elsewhere): hand-holding and too much text (part of the same problem).
The flying was pretty pointless, I get you have to travel, but after a while, it just became an extra step between warp points takig up uneccesary time (yes, I am missing actual warp points). The owl statues in Majora's Mask were great, that's how you do warps.
But another thing I wanted to add.
When I had played through Skyward Sword (done everything except last boss), without use of a guide, or without excessive exploration, I was only missing 1 heart piece. The mine cart race (I didnt know there was a race there after I completed the area).
So, where did the secrets go? Always before, when I finished a Zelda game, I had tons of stuff left to discover. Majora's Mask, OOT, WindWaker and TP has lots of heart pieces everywhere, cool stuff like skulltulas, getting all the masks, finding all the treasure maps, etc.
After doing the main quest in Skyward, the game was pretty much over, nothing left to discover, or try; other than to play the boss challenge again and again.
Where did the secrets go?! The goddess cubes werent very secret at all, they were mostly super-easy to find, and after you got dowsing, well, then it just took travel time. I LIKE SECRETS!