I only called it a shop because you use "coins" to unlock them. But the coins are gotten for completing random challenges around the world, and it functions as any other "levelup" mechanic in a game.

I don't even think the "need to come back later" mechanic is bad. Its just not well explained to you that you are missing a pretty crucial part of your kit you will unlock right after the tutorial is over. Nor that certain ones are just regular upgrades, while others are hugely important if not required for many challenges. Meaning you can accidentally buy a bunch of the "wrong" things and slow down your progression massively without knowing. Not helped by the tooltip not explaining well that the "spears from the ground" ability isn't just an AOE attack, but allows you to gain height in mid-air during glides which is its primary use.

So, its less of a mechanic issue with the game and more of a failure of communication/tutorial that makes the first couple hours sometimes fall flat for people who don't stick it out to realize what they missed. Especially as while the shrines will tell you "hey you lack the ability needed here" (though not which one), but the overworld challenges don't always.