Haha, I like your idea.
I myself have given some thought to the LoZ timeline and have it mostly worked out. A friend and I are eventually going to write a sort of history for it. But my basic order is thus.
---Minish Cap----4 Swords----4 Swords Adventure----Skyward Sword?----Ocarina*
*Timeline split. One timeline follows Adult Link, who appears after 7 years of Ganondorf's rule, gets shit done, beats Ganon, then disappears never to be seen again. I call this one the Upper timeline, because it's sort of the main timeline, and everyone always puts it above the Child Link timeline.
The Child Link timeline is the 'new timeline', which branches off the main timeline because Link was allowed to return to his childhood. Then they save Hyrule, because even though he's a 'child', he has the experience of Adult link. Hyrule beats Ganondorf before he takes over, with Child Link's help, and then captures him and sentences him to death (Cue Twilight Princess). I call this one the Lower Timeline
Upper Timeline: /----------------Wind Waker---Phantom Hourglass-------------Spirit Tracks
Lower Timelins: \-Majora's Mask----Twilight Princess-----------------A Link to the Past--Link's Awakening-----------Oracle of Ages/Seasons---------Legend of Zelda (original)----Adventure of Link.
I'm going to nerd out and explain some of my placements for these things. First off, The Minish Cap may be an odd choice for the 'first' of the series, but there are a few things. First off, it follows the story of "The Hero of Men", who hasn't appeared in any game thus far. Secondly, there is no master sword, implying MC is before SS (creation of Master Sword, from the little tidbits we've gotten) or after A Link to the Past, where it is implied the sword is put to rest for a long time. Also important, MC is linked very closely to the four swords trilogy, thereby implying that they group together in the timeline. In a nutshell, Ganon as an evil demon appers for the first time, is defeated by the Hero of Men and sealed within his weapon of choice, the Trident. In celebration of the hero, every year there is a tournament, and here begins MC. Vaati wins the tournament, opens a treasure chest full of all the demon's (Ganon's) minions, unleashing them upon the land. Vaati tries to take over the world, etc. Defeated and sealed by the Four Sword. But the four sword apparently is not a permanent seal (also important later). The seal weakens and Vaati is realeased from it, causing trouble, stealing princesses, etc. Another Link seals him again with the Four Sword. Then 4 Swords adventure, and Dark Link (first appearence in this timeline, probably created by a sorcerer) tricks Link into takeing the sword, frees Vaati, oh no, more evil. BUUUUUT, there's a twist. Ganondorf (at this point, ONLY the king of the gerudos, not Ganon yet) planned this, and released Vaati on purpose (Probably created Dark Link to do this). While Link focuses on Vaati, Ganondorf breaks into an ancient pyramid housing none other than the Trident of Darkness, containing Ganon's spirit (and a whole lot of power.) Ganondorf takes the Trident, thereby forever binding himself to the demon spirit Ganon. (See, that's why this trilogy fits so well first. Ganondorf is always refered to as just the King of the Gerudos in FSA, and then gets the trident, and only then can turn into Ganon proper.) Vaati was killed properly this time, once and for all, but Ganon finally appears and takes charge. Link beats him and seals him with the Four Sword.
But wait, remember how the Four Sword isn't a permanant seal? The gods remembered that too, so they make the Master Sword, evil's bane. This is probably where Skyward Sword will fall, but I have to wait until it comes out to see for sure.
So then we get the master sword and the eventual fading of the seal. So Ganondorf is reborn again through Ganon's power, and wins the King's heart for the Gerudo. Then Ganondorf kills the king, and lol ocarina of time. The Triforce, before this point undisturbed, is now split into its three parts by Ganondorf's imbalance.
So, for the Adult Link Timeline, Link comes, then goes as soon as Ganon is sealed within the Sacred Realm. The Hero of Time, he is called. Because of this one time, people start believing that a Hero will always travel in time and save people at the times they need it the most. Anyways, the Hylians rebuild, and all seems good for a time because Ganon is sealed, appearently for good. But then, somehow Ganon gets someone to sneak into the Sacred Realm and kill the sage of Forest and Water (A Kokiri and a Zora, ancestors to the Kokoroks and Rito). Before this betrayer gets too far, he is stopped. But the seal was now weakened enough for Ganon to seap out and threaten the world. The people pray, but the Hero of Time does not appear, and no Hero steps forward. So the gods intervene, freeze time down below, tell a few people to go to high mountains, and they drown Hyrule.
Enter Wind Waker. Lots of time has passed and still there are only four sages. So Ganon gets enough strenght over time to send out another Ganondorf reincarnation. More trouble, Link unsheaths the Master Sword to defeat it, but doing so fully breaks the seal from Ocarina of time. Ganondorf is fully unleashed, but Link finds the sages of Earth and Wind, to replace those of Water and Forest. Then the Sages are complete again and the master sword works, and Ganondorf is sealed with the Master Sword, Evil's Bane, in the depths of the Ocean. This time it works properly, and it seems Ganon is finished.
The Hero of Wind sails onward, enter Phantom Hourglass. Funnily enough, both Phantom Hourglass and Links Awakening are dreams, parallels across the 2 timelines. The Wind Fish and Oshus are sort of like 2 iterations of the same thing in different timelines. Just thought I'd point that out. Anyways, after phantom hourglass, Link and his crew find a safe new land and start a new Hyrule. This one is where Spirit Tracks occurs. End of Upper Timeline
Also of interest, it is a potential that this "new Hyrule" is stormed by Ganon, the story told by the original Legend of Zelda. It makes sort of sense, because it would explain why the Hyrule did not have a castle, or any sort of real buildings. I don't think this is where it falls though, but there is very little story in the original to tell one way or the other exactly where it falls.
The Lower Timeline splits off of the main one because The Hero of Time returns to his original time for good. (The time travel in Ocarina is all part of the upper timeline, because link changes things in his child time that effect the adult parts, but it's all kept to one timeline. The time he returns for good starts a completely separate timeline. Link returns, defeates Ganondorf, who is sentanced to an execution. The execution is botched, however, becasue Ganondorf still has the Triforce of Power. He's sent to the Twilight Realm in a last measure of desperation, after killing a Sage's apparition (not the sage itself)
And that seems to work for a time. This rather important Link (Only Link to ever defeat Ganon twice in his lifetime) lives a normal sort of life, except for the 3 days he lived over and over and over and over again in Majora's Mask. Truely, he is the Hero of Time. He did quite a bit, because of all the time travel, and thus was a sword master. His spirit, ever battle ready, becomes the Hero's Shade (Wolf Link Ghost guy).
When Ganondorf convinces Zant to usurp the Twilight Realm, another Link must save the day, this time Twilight Princess. Ganondorf is in his full power (as he was never sealed by the sages, only sent to the twilight realm), and still has the triforce of power. He can even defeat the Fused Shadows, which are all the magical strength of the sorcerers originally banished to the twilight realm. But, he falls again to the lovely combination of Light Arrows and the Master Sword. However, the sages are not invoked, and so it is only Ganondorf that is killed. Ganon falls back, and spends some time planning after such a failure.
Eventually, another Ganondorf is born (Ganon's favorite form when becoming a human). Sometime between Twilight Princess and this point, the Triforce is returned to the Sacred Realm. My guess is that after Ganondorf's defeat in TP, Link is able to take the Triforce of Power from him, and then whoever had the Triforce of Courage (Perhaps Link?) and Wisdom (Probably Zelda, since this one tends to be passed down across the generations of Princesses) were found and all of them returned the Triforce to its proper place, the Sacred Realm.
But regardless, another Ganondorf is born, again king of the Gerudos. (This is actually pretty easy for lucky old Ganon. The Gerudo are all female except for one male every 100 or so years. All Ganon has to do is use some sort of dark magic to make that male into a Ganondorf reincarnation, and he is automatically king of the Gerudos.) So, this king of thieves accidentally 'stumbles' upon the Sacred Realm (Ganon knows it's not sealed as well as it once was in Ocarina) and enters it. There, he finds the Triforce, whole and proper. The band of thieves turn on each other, out of greed for power. Little do they know that they have to contend with the King of Evil, who's a lot more powerful than mortal men, even in his current state. Naturally, Ganondorf is the sole survivor, and approaches the Triforce. Ganon(dorf) learned from his earlier mistake, however, and when he grabs the triforce, he is much wiser and courageous than he once was. He is balanced enough to get the Triforce in its entirety, allowing him power to make any wish he desires, at long last (long last for him, at least. He's been trying unsuccessfully to gather all of the triforce for the past few centuries) He wishes to rule Hyrule. In some sort of farce on the godesses' part, the Sacred Realm is turned into a replica of Hyrule and granted to Ganondorf. It turns into what Hyrule would look like under full Ganon + Triforce control, and this Sacred Realm, the Golden Land, is turned into the Dark World. From this evil seat, Ganon sort of does rule Hyrule. But naturally, he lusts for more.
People who enter the Dark World turned into what their soul reflected. For Ganondorf, that was his true form, Ganon. But any who entered, at this point, were greedy for the triforce and monsterous in the Dark World. Ganon took control of them as an army, and eventually attacked Hyrule proper with the full power of the Triforce as well as a monsterous army. No hero was found to weild the master sword, however, and all the Sages could do was seal the realm he was in, the former Sacred Realm. Thus, the Knights of Hyrule fought for time, and at their last reserves, the sages finally sealed Ganon into the Dark World.
But of course, without the addition of the Master Sword, it was an imperfect seal. Eventually, Ganon had enough power to send an incarnation of himself. This time, he chose the form of a wizard, Agahnim. He earned the King's trust, again, and then used that position to attempt to break the seal. He almost succeeds, but before he can capture Princess Zelda, he is discovered and hindered at the hands of Link. However, without the Master Sword, he could do little, and thus, Agahnim was able to capture Zelda as Link tried to get the Master Sword. Link gets the Master Sword and confronts Agahnim, only to discover he had broken the seal. Link is sent to the Dark World... where he gathers the Maidens (Sages), and then defeates Ganon at his most powerful.
Link's Awakening is a dream that follows this.
At this point, it seems that Ganon was killed proper. Peace might truely reign. However, Koume and Kotake, weird witches that probably sealed themselves away after their defeat in Ocarina of Time, come forth to revive Ganon. Oracle of Ages and Seasons explain how they go about doing this, and they come very close. But they don't fulfill the ritual properly, for they must sacrifice a maiden pure of heart. They miss out on Zelda, and so instead sacrifice themselves. Ganon is nothing more than a brutal beast, a shadow of what he once was.
Then, (if this is where these games fall, there's almost no backstory for them), Ganon is somehow revived (though it may just be the brutal, incomplete Ganon created by Twinrova), and holds the triforce of power. He goes after the triforce of Wisdom, held in the land of hyrule. This is the Original Legend of Zelda, and it can fit in quite a few places, but none well and it's hard to say. Anyways, Link gathers the shards of the Triforce of Wisdom and silverr arrows, from a scarcely populated Hyrule. He is defeated, and then follows the sequel, The Adventure of Link.
I'm not sure on this one, but I'm putting it here because the triforce tidbits don't make sense after Wind Waker (it would happen in New Hyrule, but the triforce was left in Old Hyrule), nor does it fit before Ocarina, because Ocarina was the first time the Triforce was discovered and scattered. So, it has to fall in the Lower Timeline, I think. Yet, it does not seem to fit before A Link to the Past, because that Hyrule was well populated. Thus, it must fall sometime after A Link to the Past (and probably the Oracles). After Ganon's fall in ALTHP, the triforce probably scattered to the most worth recipeints of the parts (Courage to the hero, Wisdom to the princess, Power went somewhere.) Eventually, Hyrule collapses into the wilderness we see in Legend of Zelda (original). Sometime, Ganondorf is revived properly (it's possible, as seen in the Oracles), and imbued with the triforce of Power once more. He goes for Wisdom, but is defeated one last time by Link. End of Lower Timeline.
tl;dr. I think I have the Zelda timeline mostly fleshed out. There are lots of connections to be made, and I pretty much summerized (briefly) all the happenings across and between all 15 games out, with some rough ideas for Skyward Sword's placement.