I have always had a couple of complaints about OOT's item progression. The fact that bombs (really the bomb bag) are a dungeon item bothers me. I don't know if this is right, but from all the other Zelda games I've played (1,2, ALTTP, LA, OOT, MM, OOA, WW, TP, PH, and ST) only OOT and PH have bombs as a dungeon item. I think it's kind of stupid that you can walk into the bazaar in hyrule castle market and see bombs but not be able to buy them. In LOZ, ALTTP, and LA you cab just find/buy them. Then in MM they go back to acquiring bombs outside dungeons but keep the bomb bag. A major problem is that this makes the game unnecessarily linear since the bomb bag is only preventing you from going to zora's domain before death mountain. You don't even use bombs Inside Jabu Jabu anyway. Also the story of the game is in no way dependent on you going to death mountain first (only Impa hints that a spiritual stone is there).
Another problem I have with OOT is also linearity related. If their were a non-glitch way to enter the Shadow Temple earlier (like if only 2/3 Forest ,Fire, Water medallions were needed instead of 3), then you could use the hover boots in the earlier temples. Anyone who has done the Shadow early glitch may have discovered the cool things the Hover Boots can do in those temples (Water especially). I just wish OOT managed its items differently. I think bombs should have been available upon reaching hyrule castle market, bombchus could have been introduced in dondogo's cavern (changing the puzzles though), and the Shadow Temple could have been accessed earlier (without glitches obviously) so that you could reap the benefits of having the Hover Boots in at least one of the earlier temples. Also the hookshot came at the right time but easily could have been put in a minidungeon inside the temple of light (at least in OOT 3d since they would have had space to fit it).
The best progression I think is in the original LOZ. Since the game is pretty nonlinear you can choose to get items early, but two of the most helpful items-the magic rod and the magic key- are in two of the hardest dungeons (6 and 8). So there is a huge element of risk/reward in going after those items early since they are so tough to get but the reward is huge. Otherwise, you can play it safe and just go through the dungeons in a more normal order to get more health to help in the later dungeons.
I also especially liked ALTTP because of how items were gained both in dungeons and outside, and they always seem to come at the right time. Link's Awakening also managed item progression well and incorporated the items into opening up the overworld (as opposed to reaching points in the story) perhaps more so than any Zelda game which I found interesting.
I liked how WW introduced a number of creative items like the grappling hook and deku leaf, and TP wasn't predictable either (I didn't see the double clawshots coming at all).
So in conclusion I say LOZ is the best and OOT is the worst in terms of item progression/order.
