Bonus dungeons sound great! You know what else sounds great (to me at least)? Having an unlockable secret altar or something, unlocked using a code gotten by defeating an alternate final boss. The altar that I'm thinking of could be one that cleanses the heart and mind of evil, but when you stand on the altar, something goes wrong and Link is plunged into the depths of his own mind. There, he realizes that the altar must have brought his dark side (Dark Link, of course) out of a dormant state or something. Link and Dark Link meet, and Dark Link would allow Link to use his power, though depending on the programming it could be the easy way or the hard way. Once Dark Link's power is in Link's possession, you are given the option to 'save clear data' alongside of normal saving from the pause menu. If you 'save clear data', you are returned to the title sequence once the save process it complete. When you load your file, which has been sent to the beginning of the game, you are able to switch between Link and Dark Link at will, and it won't be just a palette swap, Dark Link could be stronger and faster, or he could be the same as Link in those aspects, but his sword is producing so much dark magic that it's flowing out of it through the tip. This dark sword allows Dark Link to have his own version of any and all sword attacks Link has, even the basic ones. For example, the stab could fire a small ball of magic that flew forward, slashes could create sword beams, the spin attack could be enhanced, and any special sword skills could be made even more devestating. For example, if
TP's ending blow was in the game, it could be turned into the ending shock. Dark Link performs the ending blow, but if you press the button or whatever again (sorry never played the Wii
TP so I don't know what's what) within a certain timing range, he tightens his grip on his sword and push it deeper into the ground, unleashing a shockwave of dark magic across the ground for a certain radius that severely damages all ground enemies it flows beneath. Something like that.
Whew, that was a long-winded explanation of what I had in mind.