1) Continue this by giving the player more control over their character, like in Mass Effect (and most of Biowares other games, for that matter) or Fable, where you can at the very least choose your characters gender, as well as make decisions that effect the tide of the game.
There could always be somewhat pre-set characters that are highly customizable. Instead of a female Link, just have a different character to fill the role. Possibly using just Zelda (though this would end up with having to weave the unused character into the plot). It would be nice to incorporate elements of choice into the game. I find if more meaningful to play the hero of the game if I have the choice of being heroic. I rarely ever take the evil path in games like Fable, but being able to choose to be good makes that all the more meaningful.
2) Toss away the original concept of Link being the player's avatar, and give him his own personality, make him talk, etc. This seems to be the direction that Nintendo is pulling in, but they're at an odd in between point where Link is not you, but has only a little personality for himself (which is probably why they started giving him partners with quirky, out there personalities, like Midna and Ezlo).
Samus Aran is getting a personality developed at long last judging by Other M. It may be high time for Link to make that leap too. But I have to say I'd rather have a highly customizable Link than a talking Link. Even with full voice acting (which is way overdue), there just seems something... wrong with Link talking. I guess I'm not crazy about talking protagonists.
