I would take out Zelda (believe me on this one, it'd work out just fine; didn't Majora's Mask succeed?) [EDIT] or if not that, remove Hylia from the game completely, within the lore and all that jazz. She's the cause of Zelda's uselessness in this game, really.
I would add in more regions, and remove those stupid barriers that make it so you're confined to that region then have to go back to the sky to get to a different zone. That's just ridiculous on Nintendo's part.
I would add in a few dungeons here and there, but make them especially difficult.
Add in more enemy types, increase the amount of difficulty enemies on screen and decrease the focus on "get past my guard lulz" within sword combat.
Erase Demise and Ghirahim -- Demise I just can't wrap my head around, and Ghirahim is more of a clown than a villain. He doesn't even do much throughout the course of the game, neither does Demise. Neither villain makes it seem like I *should* save the world, because there is no sense of urgency with either villain (besides the very end, and that incidentally is when we close up the real threat >_> ).
There's much more, but I can sense someone is going to dissect my post so I'll keep it short.