I highly agree with Axle The Beast with the fact that the best option would be for Skyward Sword to try something new, a different major collectible, but also a different style of collecting, not putting Gold Skulltulas scattered along the overworld (which kind of copied the Seashells), or a mini-dungeon to go hunt thirty Gold Skulltulas.
But, if I had to choose one (although I only have two options because I've never played Twilight Princess), I would definitely choose Ocarina of Time's Gold Skulltulas, because of their quantity and the way they were scattered, following certain systems or just being randomnly positioned somewhere.
Why? Because collecting a hundred Gold Skulltulas is a lot of fun, and is a really heavy task to accomplish, which I love, being so that I love side-quests and most importantly major side-quests. I also liked how the rewards were each time better as you collected more Gold Skulltulas, which encouraged you to try to take the reward (although the last reward is... well, I won't spoil it, but I didn't really like it). You also had the benefit of getting things you could use latter in the game, that is, the wallets and that stone you get when you hunt down twenty Golden Skulltulas. The stone revealed a lot of secrets, which is something very rewarding, and the wallets allowed you to store a lot of money, so you could buy items of, for example, one hundred or two hundred rupees, an amount you couldn't pay if you still had your limited ninety nine rupees wallet.
I also choose this option over the Golden Skulltula Houses because all of the Golden Skulltulas in Majora Mask are concentarted in two places. This makes them easy to find, as they are limited to a realitvely samll place. You also knew ehere to find them: if Majora Mask would hsd gotten more Golden Skulltula Houses, and if they would have been really well hidden, I think they would have gotten my vote. It would also be a positive plus if some more Golden Skulltulas would have been scattered over Termina.
So, as already stated, my vote goes to Ocarina of Time's Golden Skulltulas.