The main flaw that Skyward Sword had, in my opinion, was the exploration. Not just in the sky, but on the surface as well. Exploration was limited on the surface; so limited, in fact, that we actually had to return to the sky in order to access the different regions. Kind of reminiscent of most 3D platformers, huh? I really do not want Zelda to become a level-based game like the Mario series. I like being able to just wander around and look for stuff, something Skyward Sword admittedly failed at. Yes, we had to search for the Goddess Cubes, but most of them were in plain sight. And the ones that weren't really weren't difficult to find. Then there's the boringness of looking for the corresponding Goddess Chests, most of which are just sitting there on a little rock in the sky. That is actually another complaint I have with the game, that of course being that the sky was too boring.
For something as expansive as the sky, the islands definitely should have been bigger. Each one should have had a puzzle on it in order to find the Goddess Chests, like that one island in the Thunderhead did. I mentioned the exact same thing in
This Thread though, so I won't go into detail about it here.
So all in all, Skyward Sword's main flaw was its exploration. It excelled in many aspects in my opinion, but both sky and land-based exploration was a bit of a drawback for me.
