Manual Jumping

I think the forward somersault/rolling attack needs to be done away with and replaced with manual jumping. Of course the auto-jump from ledges could remain for the purpose of leaping from platform to platform- these jumps would be used for reaching higher ledges.

Jump height could be increased by collecting Roc's Feather; jump distance could be increased by upgrading to Roc's Cape.

Sword Controls

Swinging the Wii Remote to control the sword is actually a fine mechanic that I don't think needs to be changed too drastically. The main problem in Twilight Princess was that Link's sword moves were too powerful compared to the enemies' usually slow movements and complete lack of armor.

The current Hidden Skill set is also good and doesn't need to be changed or added onto. Any additional special skills might make Link even more powerful compared to enemies, which is something we don't need. However:

Finishing Blow - Because I think a manual jump needs to be introduced in place of the rolling attack, the Finishing Blow as seen in TP could be replaced with the Down Thrust (A to jump, then A in the air).

Aerial Sword Moves/Up Thrust - A natural consequence of adding a jumping mechanic. Swinging the Remote in the air could result in simple aerial sword swings; swinging the Nunchuk could result in an aerial spin attack; pressing B could be used to perform an Up Thrust.

Shield Controls

Keep auto-shielding while targeting; otherwise there's no real button for it.

Change Shield Attack to holding C (while targeting) plus shaking/moving the Nunchuk so that it is easier to perform than in Twilight Princess.

While holding C with the shield out (if nothing is targeted), the option could also be given to point the shield with the Wii Remote so that Mirror Shield puzzles and the like can return.