Crazy thought suddenly came to me while I played Mario Kart - what if Mushroom Kingdom is in the far flung future of the the world of Zelda; we've already seen how strange the New Hyrule is... I mean the Princess was named Zelda by tradition, but that doesn't mean that tradition would last forever. Furthermore evolution could explain alot of the changes to their physical forms. Evolution is proven in Wind-Waker.

To explain the changes between Mario and previous Link's I'd like to point out that Link's name is usually considered a stand-in afterall, and its not like he's never worn other colours. Who know how the hero's incarnations could have changed over-time? As for Mario encountering different Links, they could be look-alikes as in Mario's games ther could easily be a full blownn cult of the hero; again the makings of such a cult existed in Wind-Waker (Triforks and Toon Link's birthday robes).

It'd explain Zelda foreseeing Mario. It'd also explain Link's dreams in Link's Awakening foreseeing so many Mario enemies. It'd also be a divine irony, and Zelda games love those, that Link's younger green grabbed brother was a heroic coward.

Adding more to the theory the sprixies are the fairies from zelda evolved but after all that shit happened (The great flood) they locked themselves into an alternate world and evolved separate from humans.

Wow that's actually such a cool theory haha
MIND BLOWN

But hey, thats just a theory! A game theory!

Makes sense; fairy fountains (and especially the Queen of Great Fairies) suggest to me that like the Sidhe/Fae they inhabit multiple planes and its not like species in Zelda have never been transformed by higher powers before (The Kokiri and the Koroks being transformed by the Deku Tree springs to mind). But I may be forgetting some part of Super Paper Mario. - Assuming the whole Paper-Verse is a result of the split timeline.

OMG!

O_O

So is Metroid in the far far future then and Samus (who is a blonde girl) is actually Zelda looking for her Link, who has been infected to be the corrupt Samus?

The future of Zelda has Link and Zelda bring arch rivals?

Your theory of Zelda as Samus is interesting but we have evidence that atleast myth of a bounty hunter exists by Mario's time. She or another person with a suit that LOOKS like hers has appeared. If you wish to claim the Goddess Hylia can traverse space as the Golden Goddesses once did and incarnated as Samus as some point in time I'd suggest it had to be during a gap-era in events on that world, which I suspect Link/Mario is bound to. 

If you feel thoroughly convinced that Samus's trend for intellectual analysis and natural warriorhood suggests she is too perfectly in line with how the Goddess Hylia would incarnate in a space setting then I put forth the suggestion that it could have been prior to Spirit Tracks as Zelda wielded the magical equivalent of Power-Armour with ease. It would also be very ironic if the time Hylia died as Samus and reincarnated as either Peach or Zelda was from her crashing her ship into Kong Country or atleast what would become Kong Country.

I must concede to you that it would explain why, at some point, Samus's armour obtained the same cult status in the modern Mushroom Kingdom that the armour of the hero of the Ancient Hyrule Kingdom did.

If you really want to suggest though that Link was dragged into a space environment by the Goddess then there is an argument to be made that he reincarnated as Kirby. Mostly though that arguement would be based on the fact that Kirby shares many traits with Link, atleast in terms of weapon-adaptability, his sword costume, and the fact they are both suggested to be destined for grand heroism (the Star Warriors being chosen by the interstellar Gods and Goddesses makes sense).

Actually some of Mario Galaxy's settings would work fairly well as settings for Kirby. But once you start pushing the idea of the Gods and Goddess traveling through space you end up bringing in Palutena thanks to Uprising and that seems messy given how eager that setting is to tell you its a game. Then again you could just put that off as her being the version of Hylia from one of the other universes from Super Paper Mario, which I guess makes sense when you consider Verdi said the Metroid esque creatures weren't Metroid's because this was a totally different universe. - Unless she was just being petty and didn't want to admit she was a planetary deity and not the Goddess of All Nature which kinda fits her too and means Hylia and Palutena cohabit the same universe. 

Ofcourse then you get into this whole thing of whether Pit inspired Hylia to reach out to the mortal Link, or Hylia's adoption of the mortal Link inspired Palutena to create Pit.

That was my exact thought while reading this! XD

Also, I thought of this episode, the everything is connected episode:

https://www.youtube.com/watch?v=blaX_eMz3Qw