First things first: There won't be any Triforce theories here because enough's been said about that already.
Theory #1: The Sage Medallions were originally going to be used as C-button items to cast spells.
Many people have theorized that the Sage Medallions that you get for completing the temples in Adult Link's world were originally going to be used as items because of early screenshots that showed the Forest Medallion equipped on Link's C-Buttons. Several websites have reported on this and include pictures as proof, such as Zelda Wiki.org. According to that site, the Fire Medallion would have had the power of Din's Fire and the Spirit Medallion would have had the power of the Lens of Truth.
However, you do not have to ever hack the game, play a beta version, or talk to a programmer to see extremely strong evidence that this theory is absolutely correct, as one remnant of it still exists in the final game.
Take a good careful look at the symbol on the Fire Medallion. It's a three-pronged flame (tilted 45 degrees clockwise in the textbox version). There is one other place in the game where that symbol appears.
It's on the pedestal that's in front of the Shadow Temple's entrance.
It is quite clearly the same three-pronged flame tilted at a 45-degree angle, just as the symbol on the textbox sprite of the Fire Medallion. But why is it there?
When you first get to this area, the torches are unlit and the entrance to the Shadow Temple is closed. You are supposed to stand on the pedestal and use Din's Fire so that all the torches are lighted at once, which opens the gate into the temple. Because the Fire Medallion logo is there, it's abundantly clear that the original plan was for Link to use the Fire Medallion while standing on the pedestal. This idea was apparently abandoned when the powers of the medallions were taken from them and given to other items. But the symbol remained even though Din's Fire has no such symbol associated with it (not that you need to have this puzzle's solution spelled out for you anyway).
The strangest thing is that since the Shadow Temple isn't accessed until quite late in the game, it suggests that either the "Medallions as Items" idea wasn't scrapped until late in the game's development, or the Shadow Temple was finished early.
Theory #2: The Fire Temple is Specatcle Rock Dungeon.
When you enter the Death Mountain Crater, you can see two very tall, dome-shaped rock formations sitting right across from one another. Smoke is billowing out of their tops and a Heart Container Piece rests on one of them. They are never actually mentioned by name, but I highly suspect they are supposed to be "Spectacle Rock".
As you may already know, Spectacle Rock first appeared in the original Legend of Zelda for the NES, in the Death Mountain area of the overworld (see left screenshot). It was the entrance to the 9th and final dungeon in the game's first quest. It reappeared in Zelda 2: The Adventure of Link, again in the Death Mountain area. This area of Zelda 2 was meant to represent the overworld map of The Legend of Zelda (right screenshot, although one of the rocks has been destroyed). (See this composite map from CB007 and this page from the NES Atlas from Crawl for more information the Zelda 1 overworld integrated into Zelda 2.)
Spectacle Rock would again play an important role in the Death Mountain area of The Legend of Zelda: A Link to the Past for the Super NES.
So, as you can see, where there is Death Mountain, there is always Spectacle Rock. Therefore, I feel it's reasonable to believe two giant dome-shaped rocks in a place called "Death Mountain" are indeed, Spectacle Rock. Also, look at their shape on the map in the bottom right corner (the red triangle is between them). A little lopsided, but just like their past representations, they certainly look like a pair of eyeglasses.
Oh, but this is not all...Prepare to have your mind blown...
Take a look at these maps of the Fire Temple. It certainly does look like the dungeon itself is supposed to be inside those two giant rock domes. Look how it's split into two halves, each ascending up to a circular room at the very top. The one on the left has the Megaton Hammer, and the one on the right is the area I like to call "the Top Secret Area", where there's a chest with a Huge Rupee and a Gold Skulltula.
The only problem is that I'm not quite sure the entrance to the Fire Temple is in the right spot for this configuration to make sense (it seems, for where it is located, that the temple should be in the walls behind the domes). But aside from there being no reference to Spectacle Rock in the dialogue, I still believe it's safe to think of this as being "Spectacle Rock Dungeon".
Theory #3: Gerudo Valley was originally going to be accessed by Child Link.
There is an overwhelming amount of evidence in the game to support this theory.
If you hack or glitch your way into Gerudo Valley as Child Link, one of the first things you'll probably notice is the additional Heart Container Piece on the platform right above where Adult Link gets thrown into a jail cell by the Gerudos. (This platform otherwise serves no purpose.) The fact that it's here, but not in Adult Link's world, is pretty strong evidence that Child Link was to have access to this area at some point in development.
Even some of the dialogue in Gerudo Valley is rather questionable for Adult Link. The carpenter, Jiro, calls him a "cute kid", for Pete's sake. That seems an odd thing for an adult male to call a teenager, but would make perfect sense if he was talking to Child Link.
CB007 pointed out to me that there's also the dialogue: "When you finally learn to ride a horse you should come back and try it", spoken by the Gerudo Master of Horseback Archery, referring to the archery game. This seems rather odd to be spoken to Adult Link since you are very likely to have learned how to ride Epona at this point because the only two ways to cross the broken bridge to the Training Grounds are either by leaping across on Epona or using the Longshot.
CB007 also adds that when sneaking out of the Gerudo Prison as Adult Link, you can knock the Gerudo Guards out by shooting arrows at their heads. It seems like this would be slightly more rational if you were using a slingshot instead.
Theory #4: The Forest Temple was originally going to be the Wind Temple and the Water Temple was originally going to be the Ice Temple.
There is a lot of evidence to support this theory in the game as well. The biggest indicators of this are the areas in Ganon's Castle that are based on the Forest Temple and Water Temple. The Forest Temple area has a wind-based puzzle. The fans used for this puzzle never even appeared in the Forest Temple at all (only the Shadow Temple has them).
The Water Temple area is based on the Ice Cavern instead of anything that actually appeared in the Water Temple.
It's very likely that the Ice Cavern is all that remains of the actual planned Ice Temple. Perhaps an entire dungeon full of ice-based puzzles was just too hard to do? Or someone just liked their Water Temple ideas more?
I'm willing to bet dollars to donuts that this change-up in development is exactly why you can never thaw Zora's Domain. Sheik tells you that the reason Zora's Domain is frozen is because of Morpha in Lake Hylia's Water Temple. But Lake Hylia, despite being closer to the so-called source of the problem, is not frozen at all. Suffering a drought, yes, but not frozen. Beating Morpha, as you already know, does nothing to unfreeze Zora's Domain.
The more likely explanation is that the cold air was coming from the boss of the Ice Temple (now the Ice Cave), and beating it would have unfrozen Zora's Domain. But since the Ice Temple was cut, that part of the game was cut, too, and that line of dialogue was given to Sheik to explain the cold air, even though it clearly makes no sense.
On the Forest Temple/Wind Temple Theory, consider that not only do fans appear in the Ganon's Castle segment based on the Forest Temple, but the symbol on the Forest Medallion looks a heck of a lot like a fan. Hackers have discovered Japanese text stored in the ROM for an Ice Medallion and a Wind Medallion. Hacking the Wind Medallion into Link's inventory reveals it to look identical to the Forest Medallion. This could pretty much lay to rest any doubt that the Forest Temple was originally going to be the Wind Temple.
It is unknown at this point if the Ice Medallion corresponds to the Water Medallion in the same way, but consider that the symbol on the Water Medallion resembles a snowflake.
Theory #5: The Light Temple was originally going to be a playable area, but got turned into a cutscene-only area and some of its ideas were combined with the Spirit Temple.
The evidence for this one is a little shakier, but I still get a very strong feeling that the Light Temple was going to be playable at some point, but was changed so that you only ever visit it in the cutscenes with Rauru the Sage, and that its basic ideas were combined with the Spirit Temple. For one thing, it seems really strange that the Light Temple and Sacred Realm are mentioned so often in the dialogue, only for you to never actually be able to explore them.
For another, the Spirit Temple contains two completely different types of puzzles - time-based and light-based. My guess is that the light puzzles were probably originally intended for the Light Temple, and the Spirit Temple was going to be entirely based on traveling through time. But for whatever reason, be it time constraints or the inability to make an entire dungeon out of just one of these two concepts alone, the two ideas were merged into one.
CB007 also adds that Kaepora Gaebora's dialogue is a bit odd when Child Link meets up with him during his portion of the Spirit Temple. It sounds as though he is talking to Adult Link seven years later:
Hey, what's up Link? Surprised to see me?
A long time in this world is almost nothing to you is it? How mysterious.
Even I thought that the tales of a boy who could travel back and forth through time was merely a legend.
Link, you have fully matured as an adult. From now on the future of all the people in Hyrule is on your shoulders.
Maybe it's not my time anymore. Here is my last advice.
Why would Link be surprised to see him as a child when he's shown up for every child dungeon? How would the owl know Link had matured and was traveling in time if this took place in the past? Not his time anymore? That sounds like a future version of the owl. Maybe the owl was supposed to visit Adult Link in the future instead of disappearing.
There is also unused dialogue stored with the rest of the desert area text that says, "The Entrance to the Past", "The Entrance to the Present", and, "The Entrance to the Future". These may be with the desert dialogue because they were intended for the Spirit Temple. What's even weirder about them, though, is that they suggest three different time periods, whereas in the final game, Link only travels between Present and Future, not to the Past. Anyway, the owl's dialogue being out-of-sync is probably a result of these changes being made.
It's quite possible the Prelude of Light's original purpose was to warp you to the Light Temple instead of the Temple of Time. (If it's taking you to the Temple of Time, shouldn't it actually be called the Prelude of Time?) It's also the last song on your list, despite how early you learn it, suggesting the Light Temple would have been the last dungeon you'd explore before Ganon's Castle. But wait, there's more on this one!
This is where you warp to in the Temple of Time when you use the Prelude of Light. Take a good look at the symbol on the warp pad.
Why, hello there, Light Medallion! You seem to bear the same symbol. Prelude of Light...almost definitely intended to be a warp for the Light Temple.
Hell, I think there could even be a strong argument that the Temple of Time itself is what's left of the Light Temple. Not only the symbol on the warp pad, but the light shining in through all the windows, and look at the carving on the door in the back that leads to the room with the Master Sword - it's a freakin' sun!!
But what would you have gotten for beating the Light Temple? Probably the Light Arrows, of course! And that would definitely be right in line with the Light Temple being the final one before Ganon's Castle since you wouldn't need them until then. But ah, that's quite enough speculation for one day.