Koh -Vs- Ocarina of Time

[Terminal Devastation]

I'll admit any of the "get upgrade versions" to preceed are just linear keys that add nothing to the game.

But when it comes to the Hookshot/longshot, it is in fact, just as diverse as the grapplebeam in super metroid. (Honestly, I think you've mixed up your metroids... since Grapple beam was mostly just a area crossing tool in super metroid).
THe hookshot DOES react differently to different enemys. It stuns most, kills some (Notable mention, Large skultulas), and even grapples to Iron Knuckles (Why you'd WANT to do this is another matter). I use it to save arrows. Just like you'd use missiles in metroid to kill stuff faster, or not use them to save the missiles.
Further more... it grapples on to most wood surfaces. Sure there was visible grapple points for where you absolutely needed to go, but those are not the only place they can grapple. (TO be honest, OoT uses the hookshot better than most Zelda games, and even better than mostgames I've seen use similiar items. Only one better I can think of is Thief's rope arrow, and that's pushing similiar a lot)

Anyways... I figure that ideally, each dungeon serves as tutorial of what each dungeon item can do so the item can be using in later dungeons in more advanced methods while you're learning THAT dungeons item.
I found this to be done have decently... especially in Bottom of the Well to Shadow Temple, and Ice cave to water temple cases.

And no. You can't fault them for not having a brand new idea years in advance. (For not trying to have so much item overlap... maybe you can)
It's like faulting the makers of Pong for not making Portal 2 back then.

For the record, I'm just trying to show you're not entirely correct. I agree things could be better, but I strongly disagree that fact makes the game bad.

[edit] In regards to comparison to metroid... Yeah, Zelda could learn a lot from metroid... but Zelda's formula isn't as flawed as you seem to think. Zelda's formula's flaw isn't the formula use item you got in the dungeon based around it. I may have mentioned it earlier, but that can serve as a fluid tutorial. The flaw in the formula comes from the linear nature of the order of dungeon progression. There is less of a sequence in Metroid.
If one had some more choice of which dungeon to go to, and say the items from each dungeon merely open up more possibilities to solve a problem in the remaining dungeons while lacking said items from didn't mean you couldn't complete or get to a dungeon, the zelda formula start to excel... more than Metroids formula. Because again... each dungeon would serve as a hidden tutorial for each item, and you'd just have to choose which to learn first.