Well to my knowledge in the games Dark Link was created by Ganondorf, but in Twilight princess the two dark links were only part of a vision created by the light spirit Lanayru. As for the main villain they couldn't go wrong with using Ganondorf again, but I think it would be interesting if they came up with some one new. I'm just noticing that from what I know is that the Skyward sword eventually becomes the master sword and the sword and ganon are in the same games so wouldn't it be plausible for there to be a completly different villain, one that was so evil they had to create the Master sword just to defeat him?
Just another thought, what if the link you play as in the game is related to the golden wolf in twilight princess. What I mean is that in the twilight realm link took the form of a wolf because he has the Triforce of courage. So why does that armored knight take the form of a wolf before he teaches you the hidden skills and (spoiler) when he teaches you the last skill he calls Link his son so could that mean that you are really playing as the Golden wolf? I think that it would be an interesting twist to the series.
if u look at the knights sword and sheild they are similar to links in majoras mask also in majoras mask when u finish the game link still went lookin for his friend in the lost woods and once u die in the lost woods u turn into staflos... which the knight in tp is
Wouldn't it be interesting if the plot was about the twili being banished to the twilight realm for attacking the sacred realm? If I remember correctly Oot was the first game where ganondorf managed to get into the sacred realm and it was sealed by the master sword. Since the master sword is created in Skyward sword wouldn't that mean that the sacred realm isn't sealed?
Also heres another thought, what if the main villain was the first King of the twili. Before the fight with Zant, Midna mentions that they lost their first king to greed, so could he be the one that is behind it all?