There are tons of good reviews going around for Skyward Sword and it is justifiably so. I just 100% completed Skyward Sword and also recently 100% completed Ocarina of Time 3DS so I think it is the perfect time to compare the two and see which one comes out the victor based on a set of 7 different categories. There are some minor spoilers in the comparison so read at your own risk. I don't spoil the endings or anything major, but if you don't want to know anything about either game, then I guess you shouldn't be reading this comparison. :)
Skyward Sword (Wii)
Ocarina of Time (3DS/N64)
Winner
Story
Pros
Great starting story for the franchise.
Does an amazing job showing the chemistry between Zelda and Link at the beginning of the series.
Story never really has any dead areas where you wish you could by-pass it entirely.
Cons
Beginning of the story can take a long time to develop. It's very story-driven/character-driven and takes a while for you to get your sword and get on your way.
Pros
A Timeless Classic. Boy travels through time to save the one he loves.
Cons
Character development is good, but is no where near as good as Skyward Sword.
There are some locales the story drags along... like the 6 medallions quests.
Skyward Sword
Environments / Levels
Pros
Timeshift stone levels are amazing and very creative.
3 world setup is very diverse.
Skyloft is a place you'll want to keep returning to throughout your quest to see what's new. Feels like home.
Cons
Only 3 main worlds to go to. Even though they have sections, it still seems a little small.
Not enough things to fly to or do while flying.
Pros
You can fish and it is fun!
Game brings you to some exotic locations including Gerudo Desert, Lake Hylia, and Zora's Domain.
Cons
Contains one of the most annoying temples ever (Water Temple), although this was semi-corrected in the 3DS version.
Skyward Sword
Characters
Pros
Great shopkeeper characters. You actually WANT to talk to them as they are done so well.
Main characters are great and very unique, including Groose, Zelda, the Headmaster, etc.
Beedle makes a return, and who doesn't love Beedle right?
Cons
Fi can be annoying at times but no where near as annoying as Navi.
Pros
Ganondorf and Zelda make appearances.
Happy Mask Salesman is quite eccentric.
Koume and Kotake are hilarious bosses.
Gotta love Dampe...
Cons
Shopkeepers aren't that lively at all. Very generic.
Navi and the owl can be two of the most annoying characters ever.
Princess Ruto is always COMPLETELY annoying... carrying her everywhere and just being a pain.
Skyward Sword
Controls
Pros
Wii Motion plus is the best thing to happen to Zelda in a long time.
Quick access to weapons with a flick of the wrist while holding B is awesome.
"Z"-targeting is still here.
Don't need to stand to play the game (I sat the whole time and still had a blast).
Cons
Wii Motion plus can need to be "centered" every now and then.
I haven't really found a need for the shield in the game, but it can come out when you don't really need it sometimes.
The minus (-) key is sometimes hard to use if you need potions.
Pros
Purists prefer no Wii Motion plus and want to have everything mapped to a button for 100% control.
Introduced Z-targeting to the 3D gaming world.
C-buttons were great for shortcuts to items.
Cons
Was a pain to put on various boots when you needed them (corrected in 3DS version).
Doesn't have the motion controls / 1:1 controls that Skyward Sword has.
Skyward Sword
Graphics
Pros
Game is beautiful and it has a great design to it.
Art style is perfect for a Zelda game... it's a blend of Twilight Princess and Wind Waker.
Graphics are vibrant and look very artistic. Up-close visuals are particularly pretty.
Cons
Game looks a little "blurry" / choppy when you look at background environments. A limitation of not being in HD and it can be distracting at times.
Pros
N64: Amazing graphics for an N64 game. Was a tremendous achievement for its time.
3DS: Graphics look amazing and the 3D effect is stunning. Looks 100x better than the N64 version.
Cons
N64: Game hasn't really aged well graphically with new technology around (expected).
3DS: Game looks amazing but it is only at a low resolution. Still can't match Skyward Sword's art style.
Skyward Sword
Music
Pros
Has the traditional Zelda music... and it is enhanced!
Harp music isn't bad. Sounds pretty.
Cons
Nothing all that memorable from the harp songs. Music is no where near as memorable as Ocarina of Time.
Pros
Some of the best music ever in a video game.
Ocarina songs are timeless and you never forget the button combinations!
Cons
None
Ocarina of Time
Gameplay / Weapons
Pros
Game has a fun flow / general progression to it. You earn items that help you progress farther in the game.
Lots of side quests to be completed.
Borrows a lot of gameplay style from Ocarina of Time.
Requires you to use Wii Motion Plus and unique strategies to beat each boss/enemy.
New unique weapons to use. The flying beetle is the best new item yet!
Cons
Has some repeat weapons from prior Zelda games (expected).
Has a good number of fetch quests as well which can be annoying.
Pros
Game has a fulfilling progression to it. You earn items that help you progress farther in the game.
Traveling through time mechanic is fun and creates some very unique puzzles/situations.
Good number of side quests including Gold Skulltulas and the Biggoron's Sword quests.
Cons
Has some fetch quests and some of them can be annoying.
Note: I could have went into more specific details as to why Skyward Sword is better, but I wanted to keep this comparison as spoiler-free as possible.
You may be surprised to see Skyward Sword beat Ocarina of Time in a head-to-head comparison. Ocarina of Time is considered by many to be the greatest game of all-time and rightfully so. However, once you strip away the nostalgia and the history, you can see that Skyward Sword takes everything that Ocarina of Time does and makes it better. The characters are all unique and have lives of their own throughout the day, the controls add a lot to the gameplay, and the story and graphics are what adds up to a great Zelda game. Ocarina of Time may go down as the greatest and most impacting game of all-time, but Skyward Sword is ultimately the better Zelda adventure hands-down.
If you want an alternative opinion, IGN did a survery asking readers what they thought: