DARK MASTER
The Emperor
Could Skyward Sword just have been better in every possible way?
Could Ocarina of Time have been even better had we seen Ganondorf actually take over Hyrule during Link's nap time.
@Spirit to fully answer your question is well beyond the scope of a normal reply, like seriously a whole editorial could be written on just a single game, but I would like to point out if they actually added scraped content into OoT3D (which I'm recording currently) that could meaningfully improve the experience. Something statements could be said about other games you mentioned, like Wind Waker. What dungeons in particular people would like to see added from beta?