Yes, I'm shamelessly copying this from a topic in which I posted on the Wii U board, but I put much thought into its creation:
I do not think OoT is overrated, though I do stress viewing it in the context of its time. Many gaming classics can be found in the SNES and PS2/GCN eras--not so many on NES or PS/N64. This is because the latter were so experimental in laying down the foundations for game design, while the subsequent generations more or less were spent perfecting those foundations.
OoT is unique compared with just about any of its contemporaries; Super Mario 64, FFVII, Metal Gear Solid, and GoldenEye have all aged in comparison with the innovations and advancements brought about in their respective genres. OoT's gameplay still holds up as incredibly good today. My thesis is that this is because of its striking "unity of vision" informing all of its elements, a unity only achieveable during times of highly experimental game design pioneering.
If I was to be asked my favorite Zelda, I would say Twilight Princess, and yet I acknowledge that some of its components fit together only awkwardly. And I dare say that this is so for any of the other 3D Zeldas--their unique spirits were conceived only upon the blueprint of OoT (pacing, look, type of puzzle and exploration, dungeon progress, control layout, etc), while OoT's various components are organic extensions of its foundation.
Young Link's world is a magical realm of more or less order and security; likewise the plot and dungeons spirit the player around in fairly straightforward progression. But the adult world has come to chaos, bringing with it a degree of complexity and nonlinear exploration, as well as a sense of despair and danger. These elements play back into the central time-travel storyline, so that the player feels as if he is growing and can be trusted with more freedom the farther into the adventure he travels.
Young Link's dungeons are fairly simple encounters, but they do exactly what we needed in 1998: teach us the mindset for exploration and puzzle solving in 3 dimensions. They are also organically incorporated into the world you are still exploring (e.g. you go into a tree or within a deity's belly). Adult Link's dungeons are entirely different affairs: they still serve among Nintendo's greatest level designs, each offering a unique "theme" to progression while serving as complex mind-game and navigation puzzles. Contrastly with the child dungeons, they are all abstract intrusions into the world: just "temples" of elements seemingly placed into the world. Adult Link's world lacks the order and cohesion of the child world, hence these abstracted (challenging!) breaches into the world's "realism".
My point is that the telling of the hero's story--the very essence of Zelda, if I may be allowed to put it so--comes out in every element of OoT's design. The story serves this purpose, the NPCs and environments--especially in the context of their change over 7 years--give a depth and weight to your adventure's proceedings; the soundtrack has "epic fantasy adventure" written into each of its pieces; the pacing serves its purpose; the main game length and side quest options all point to the hero's growing liberty and responsibility; the puzzles evolve into more and more complex endeavors; and the art style, ironically using the N64's limitations as an asset, provides a timeless element with its undetailed fantasy-realism approach. These all contribute to the sense of "grand adventure of the hero coming to be" and a complex of ideas centered around time imagery and eternity. These play out both in Link's adventure and in the villain's tale, of Ganondorf's origins, rise to power, and subsequent tyranny--a coming to be of a conflict that plays out in two worlds (present and future), with its result likewise effecting both worlds.
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It is the crucial moment in the timeline and the defining example of what Zelda's gameplay is all about. Those who criticize it for a lack of storytelling are too narrow-minded in what counts as story-telling in a video game.
I do not mean for my post to imply that OoT is flawless, but each aspect that, taken in isolation, we nowadays would tally as a flaw, when seen in its larger context is not a flaw but a fundamental element in achieving OoT's unity of vision and experience. Again, this is why I think OoT has held out so much better than its contemporaries (or its Zelda brethren).
I will not call OoT my favorite Zelda game, but I am indeed sympathetic to it being called the best game--the subtle distinction is key in fulling appreciating OoT's power. And, rather than with that condescending qualifier "for its time", OoT retains that power just as fully today, in a time where vast developer freedom has compromised the integrity and unity of the gaming experience. Today's gaming standards can make shallow any part within OoT's design, but they touch not the whole of the design.
If I may be so bold, what do you think?