I see no logic in a plot change....it's not like it's a different game. It is still the Wind Waker, but with prettier graphics. If Nintendo was thinking of plot ideas, then it would make more sense for said plot ideas to be used in a future Zelda game and not in one that has already come to pass. The only time adding plot to a remake of a game is if it was a game that started out with very little plot. The only game I can really think of at the moment is Final Fantasy III.
Final Fantasy III was developed before plot was really an issue in games. Back then people were concerned about making a game that had good gameplay. Plot wasn't really necessary for something to be successful....just a fun game. Mario never really had a plot, Zelda didn't really have a plot, plots were always kind of second nature. When Final Fantasy II was re-released for the Nintendo DS, Square Enix thought thought it would be a good idea to actually give names to the 4 protagonists as well as adding some back-stories. All of this makes sense as the game had very little plot initially.
Wind Waker on the other hand was developed after this plotless era in gaming. It was given it's own story, which may not be one of the best stories in existence, is still a good story for a Zelda game. To go back and change what happened in the game.....well honestly that's just stupid. Imagine if you read a book as a kid and you really liked the book. A couple of years pass and the book is re-released with a new edition. Is that book going to have plot changes? No! (Unless there's some weird censorship thingy and blah blah blah....stupid stuff.) I see literally no benefit in changing the story or adding plot points or changing plot points. The only thing that I see coming out of that is alienating fans of the original game. If you want to make a new story then do just that....make a new damn story and don't change the original.
I don't want to say this is a stupid question as I feel that's rather rude and insensitive, but I can't help but voice my opinion that this is a rather pointless question. A better question in my opinion would have been "What changes in the game would you like to see?" Adding some extra content such as optional dungeons, boss gauntlet, harder difficulty...those things are things that could be talked about and/or debated. I just feel that trying to add/change plot points to a game released for the Gamecube is just silly. It's already got a fantastic story.....and even if it didn't.....I still see no reason that the story should be changed.
Changing the story in my mind isn't really a remake, but rather a re-imaging. It's more on the lines of movies that use the same idea...but change a few things. Some example being the Karate Kid, any Super Hero movie (revamping and what not), True Grit, and The Day the Earth Stood Still to name a few. Needless to say, re-imagings are done all the time. When one media form is converted to another, there is often a little wiggle room in the telling of the story and that's fine. That being said, I don't see the point in doing this with a game.