I agree, Dark Link should get a backstory, or maybe even a continuation! I can see it now...
Ganondorf, too busy with taking over the world to fully complete Dark Link's spell-summon, didn't put in a condition to terminate him upon his death. Therefore, Dark Link just came back after Link left the Water Temple. Forced to wait for the hero to complete his journey, Dark Link feels the barriers placed upon the room to keep him inside crumble as Ganon does, and is finally able to leave his watery prison.
After he figures out the whole 'swimming' thing.