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.
