More bow combos: We got a rocket launcher and a sniper rifle. That's fine, but there was so much more that could have been done with it.
More minigames: Considering the size of Castle Town, there could have been copious amounts of minigames there. Shooting galleries, Bombling Bowling, the list goes on.
Ability to fight bosses again: Majora's Mask rocked for this. Get new items, go back to dungeon, fight boss with new strategy. What could be better?
Moblins and Octoroks: Two of the most recognisable enemies in LoZ history didn't even make an appearance. Despite Moblins being in the trailers. C'mon, where the hell were they?
That bit from the second trailer where Link gets chased by Ghoma: Do I really need to explain?