Hmm. In that form, I could take Navi's pestering. Simply because she comes with an off switch in it.
Should the Master Sword be a Chain Sword?
Nope, power sword. Power swords in WH40k come in the form of bladed weapons that cover the blade with an energy sheath, to ones that create blades of pure energy ala light sabers. They are more powerful than chain swords, and there are ones that are very old artifacts and/or infused with some of the Emperor's power and coorespondingly potent.
While taking this too seriously, if someone DID run with that idea, The Master Sword would probably be an ancient power sword with a singularity generator attached to it or something. Perhaps even having been present during the final slap fight between The Emperor and Horus and sucking up some mojo due to it (The Emperor being so powerful that things like certain Rogue Trader writs that bear his direct signature and basically indestructable. One of the novels I read had one floating through space after the destruction of the ship that was carrying it if I remember). Link's quest to get it would be similar to many other quests to recover chapter artifacts or archeotech.
That said, I have been waiting for someone to do a female Link in a game, I know a lot of girls cosplay in Link costumes.
Also given the way the world of Zelda seems to incarnate into parallels of itself, I've always thought it would be vaguely amusing to see a game where Link was the prince, and Zelda was a peasant girl who has to become a hero to rescue him.
... and yes, Navi could be forgiven on the mertis of being a servo skull. I mean heck, Mort was an obnoxious sidekick, but he worked in "Planescale: Torment" because floating skulls are awesome!