1. I would have liked a suspenseful chase scene - kind of like how the guardians chase after you, but between Link, Ghirahim, and Zelda instead. Ghirahim could be chasing Zelda, with Link chasing him as Ghirahim, and Link has to stop him before they reach a certain place, or before time runs out, because Zelda gets caught.
2. More about the Dominion Rod. I was expecting
SS Link to be the "messenger of the heavens" as Impaz said in
TP, but it wasn't even mentioned.
3. Like Link Harkanian said, I would've actually liked if Ghirahim had attacked Skyloft. I remember before
SS came out, some of us thought that he actually would because of some of the trailers. This would have been
awesome, because then the fight against Ghirahim would suddenly get much more personal, because he just destroyed your home. I was really excited about this, but it never happened, of course...
4. I would've absolutely
loved if the Gerudo had been in it. When the robot was talking about pirates taking his ship, my excitement exploded. But... I was disappointed again.
5. The creation of Dark Link. It wouldn't necessarily have to be like
this, but before
SS came out, I was thinking that it would've been cool if Ghirahim ended up turning into Dark Link somehow...