For me, the one thing WW was seriously missing was an extra encounter with Ganondorf where he goes into further detail on his past. He was there for the main event, so obviously he would have remembered things that were smudged by time. Rumor has it that there was going to be a scene where Jabun is killed or injured, so maybe that would have been a good point for storytime with Ganon? Perhaps he could even recall killing Jabu Jabu for a flashback.
That's the way I would have done it, at least: Start the game with a vague outline, Ganon himself clears up the picture, and then you get the little tidbits of lore scattered about the game. Then again, a returning dungeon would also be a good idea, so I guess I'd throw that in for good measure too.
I think WW would have benefited from just
more time spent with Ganon. It's an issue I have with almost every Ganon encounter, but with WW most of all.
This is the
one version of Ganon that seems to be propped up in a more sympathetic light, to the point where he's almost
not the bad guy, but the game glosses over those motivations in favor of a big stabby sword fight. Give me some flashbacks, some dubiously good monologuing. Maybe a point where Link hears Ganon's sympathetic motivations and his desire to
resurrect Hyrule and looks to Boat King with a look that says, "Hey, maybe we aren't the good guys in this situation."
Remember, Ganon's
entire plan in WW is to resurrect Hyrule, and the KoRL's goal is to
drown it. Leave the few survivors of the apocalypse that
he brought on to fend for themselves atop what has been stated in game to be a dead and lifeless sea.