Link would easily own Cloud even without Fierce Deity for one major reason.  Cloud can't move!  Link run laps around him and swing away while Cloud patiently waited for his turn.  The point is, real time will always out do a turn based game.

On another note, Cloud does appear in a straight to video movie.  If Link were to face off this new movement based Cloud in a world of gravity (see advent children and you'll see my point); Cloud would struggle walking or even holding up his gigantic sword.  If Link were to enter Cloud's world without gravity; yes Link may be in trouble, mostly because Link would have to learn to funtion in this world without gravity.  The point is, Advent children was a stupid movie that didn't even fallow the basic laws of science (gravity).

*votes for Link* 

First off, the idea of a split timeline after Ocarina of Time is foolish.  After defeating Ganon, Zelda tells Link to give her the Ocarina and to reclaim his lost years.  Link is then sent back to being a child.  Then in Majora's Mask, Link remembers his last conversation with Zelda, where she describes how she feels that she has known Link forever and was disappointed that he was leaving so soon.  All these memories couldn't have happened if Link's brief adulthood never happened.

Next is the distant time span in between Ocarina of Time and the Wind Waker.  So many different Heroes could not have existed in between games.  Replaying the Wind Waker a second time obviously allows the player to play the entire game in the Hero of Wind's PJs.  Another treat was being able to actually read the various Hyrulian language conversations spread throughout the game.  In these conversations we discover the King of Red Lions (Link's boat/King of Hyrule) was searching for the Hero of Time.  The Hero of Time was the last Link in the time line so the King searched for the Hero of Time so that he may once again defeat Ganon.  His time was unfortunately over and a new hero had risen to be the Hero of Wind.  Had multiple Link's existed after the Hero of Time's reign, the King would have searched for the Hero of Elements (Oracles) or the Hero of Hyrule (Original).  The Wind Waker takes place directly after Ocarina of Time and the Wind Waker, with the exception of Majora's Mask.

Of course now, we are told Twilight Princess breaks in between the two titles.  This can throw apart my whole argument, but it is impossible to tell about this new Hero until his title comes out for the world to play.  I figure that something is going to happen to this Hero that will somehow pull himself out of the Hyrulian History.  Perhaps he dies in battle, or retires early, no one knows.  A lot of questions will be answered in Twilight Princess, which makes me that much more excited.