A Pokemon? Well, that'd completely ruin the series. First of all, Link would oly be able to know four moves, which for him would be along the lines of a sword and three other items. Further more, Link would have lost all his sentience, roaming about in the wild until captured by a trainer. This segways us into my next point. The player would no longer control Link, but the trainer who captured him. Because this trainer may have little experience in life-threatening situations, Hyrule could quite possibly be doomed. Assuming control would be easier than taking candy from a baby for Ganon, as Lonk has been diminished into an inferior creature.
What if I ran home?