Problem being the only thing you can do with that wiggle room is
Open chest on rock with nothing but said chest
After activating it by finding the appropriate Goddess Cube.
Dowse or find not-very-well-hidden-Goddess cube
Not quite sure what you're getting at here. If you mean that many of them were in plain sight, then sure, but it's not like you could just walk up to (all but a few of) them with little to no hassle like the vast majority of treasure chests in Twilight Princess. Skyward Sword took the approach of "hide it in plain sight, make the route to it tricky to find", much like in A Link to the Past and The Minish Cap (I think you can see why I draw so many parallels among these games' overworlds). There were even quite a few that you couldn't immediately get, meaning you had to remember where they were and what kind of obstacles were set in place when going back to find them -- again, like in ALttP and TMC.
do fetch quests on main island, which require you to fly to more small rocks
Quests that each have their own story with detailed characters and have do different things while going to different places. Let's list the other Zelda games that have done that, shall we: Majora's Mask, Spirit Tracks. Oh, well look at that. The Wind Waker and Twilight Princess don't show up in that, do they?
upgrade equipment on main island
Which is only doable by collecting treasures on the surface. It also provides incentive to go back to the main hub and actually spend rupees, something that was completely absent in literally every previous Zelda game.
3 minigames (As opposed to the at least 5 in TP)
Um... what? Skyward Sword had 6 core minigames: Bamboo Island, Fun-Fun Island, Thrill Digger, Rickety Coaster, Bug Island, and Pumpkin Pull. There's a total of 9 if you include the Lightning Round -- a double-edged feature, with the boss gauntlet and Silent Realm challenges -- pumpkin-carrying, and harp-playing.
3 minigames? Try triple that, which is nearly double of TP's.
What there is to do, doesnt manage to differentiate itself as much the other Zeldas
It repeats itself a lot, and doesnt even bother to hide the fact that it is well
Right...
Most heart pieces are gained from obtaining the Goddess cubes, then opening the chests which there is obviously no puzzle to. The only puzzle part about finding most of the Cubes is "Use the Skyward Strike from a certain angle"
Except there are often paths you have to hunt down to get to them, as I already went over.
Everything you can do is very shallow basically.
If by shallow you mean the complete, exact opposite.
Unlike TP which simply has more to find in different ways in it's overworld, AND it's main hub.
Its main hub? What main hub? It's four provinces connected through lengthy hallways. It's also cute how you think there's more content in TP's overworld.
It's not about how much wiggle room you have that makes it linear, its what you can do with that wiggle room that counts. In SS, you cant do much that isnt the same thing over and over. there isnt much to do, therefore, its one of, if not, THE most linear Zelda
Ignoring the fact that this logic is insanely flawed -- more wiggle room is more wiggle room, period -- let's flip this on its head. By this logic, I could argue that The Wind Waker is the most linear Zelad game. It has a considerably smaller amount of content than both TP and SS, with a open, but very,
very empty overworld that's way too big for its own good. Sure has a lot more wiggle room. Not really much you can do with it, though. At least not while sailing.