I'm in a unique position. I've never played Ocarina of Time until now. You might say that disqualifies me from passing judgment on whether it or Skyward Sword is the better 3D Zelda game, but I disagree. Since nostalgia isn't a factor, I can compare the games without any previous bias. Plus, I can assess the situation a little more clearly, so it's without reservation that I say Skyward Sword surpasses Ocarina of Time in almost every way.
Before I list the reasons, I do want to acknowledge that Ocarina of Time and Skyward Sword are equals in many aspects. They both offer excellent animal companionship, do extraordinary things with music, and are highly creative games in terms of design and story. Skyward Sword is just a little better at it, or in some instances, much better. That's probably because Ocarina of Time serves as a template on which Nintendo has built Skyward Sword. The two games possess distinct looks and storylines, but they share many basic themes—but that's comparable to any Zelda. What game in the series doesn't have a mountain or volcano, fairies, or temples and dungeons? The names Rauru and Ruto have appeared in entries as early as Zelda II to later classics like Ocarina of Time, and Princess Zelda is anyone from a blonde pirate to a girl in Link's dreams. The point is that both games are enjoyable in different ways, and while Skyward Sword expands upon Ocarina of Time, it doesn't copy it. It fixes what needed fixed and improves what could have used more thought and attention.
Here are ten reasons why Skyward Sword comes out ahead. You shouldn't feel bad about saying so.
The Controls
Motion controls are notoriously gimmicky, and gamers tend to prefer them less to standard button inputs. So for Skyward Sword, which uses motion technology, to demonstrate such smooth handling over its controls is no small accomplishment. The motion-plus sensitivity syncs the player with the controller almost perfectly; every movement is repeated on screen without hitch or delay. Sometimes the movements falter, but most of the time they stay on course. Considering that button controls can be finicky, too, Skyward Sword presents some intimidating competition.
However, we're not just talking about flawlessly programmed inputs. We're talking about the depth of control the player has over Link, and that's much deeper in Skyward Sword than in Ocarina of Time. Players have the freedom to roll bombs instead of just throwing them overhead or placing them at their feet. They can strike their sword in any direction or unleash a spin attack with ease. Not to mention, running across narrow ledges is much more doable in Skyward Sword than in Ocarina of Time. Ever try to walk across the ropes to the giant Goron urn in the middle of Goron City? How slowly did you have to tiptoe to make it there, or across any narrow walkway in the game for that matter? Making Link walk or run in a straight line is less frustrating in Skyward Sword than it is in Ocarina of Time. Just head down to Batreaux's house in Skyloft and see for yourself.
Guardians
Navi and Fi are both annoying characters in their own respect. They both pop out and tell you useless hints or obvious information when you don't want or need them to, and you're stuck with them for the entire game. At least Fi helps you grow more powerful and doesn't fly to objects so that your aim focuses on them instead of the action in front of you. She doesn't shout, "Hey, listen!" either, which is a major plus.
Camera Work
The camera is more polished in Skyward Sword. In Ocarina of Time, it just looks goofy whenever Link picks up a piece of heart or another item. He gets completely cut off, and all you see is his half his head and arms holding up a gigantic item! Some might consider that a quirk, so it's the camera angles in boss battles, particularly, that can be difficult to work with. The fight with Phantom Ganon and Big Octo come to mind. In worse cases, the targeting won't even work, replacing proper line of sight with a confined view of the nearest wall.
Bomb Flowers and Other Items and Upgrades
Bomb Flowers existed in Ocarina of Time first, but Skyward Sword lets you stuff them in your bomb bag. Loading a live bomb into a cloth bag without it exploding doesn't make much sense, but that's video games for you. It's a lot cooler and more convenient that way.
Not to mention Skyward Sword provides many more versatile power-ups and upgrades. I'm continuously impressed with how relevant otherwise useless items are in Skyward Sword—like the Gust Bellows, for instance. I won't spoil anything, but you'll be using that item in an unexpected location later in the game.
Using Equipment
The simple act of using equipment is much improved from the original Ocarina of Time. Instead of assigning a limited number of items to a button group, players of Skyward Sword can choose any one of them from the B menu. It's quick and hassle-free, and you won't have to worry about flipping through menu pages.
Aiming is also a lot more manageable with the convenience of motion controls and the sizable targeting receptacle. Good luck trying to get an accurate shot out of your bow or slingshot in Ocarina of Time.
The Map and Checkpoints
Skyward Sword is leagues more approachable and user-friendly in this department than Ocarina of Time is. The map in Skyward Sword might look silly with Link's head pinpointing his location and shining a light in the direction he's facing, but it's extremely helpful. Note that this feature works on the world map and not just isolated locations, whereas in Ocarina of Time, players had to guess their location within a grid when navigating Hyrule Field or other non-dungeon vicinities.
Then there are the checkpoints. Not only can you teleport to any bird statue you've touched in any region, but when you die, all your progress remains intact. For years this has bothered me about Zelda: I'd make my way through a complicated dungeon, only to die and start over at the entrance, with all enemies revived and my latest efforts (except for keys and other newly obtained items) undone. The lax checkpoint system in Skyward Sword comes in handy very frequently, saving time and reducing my frustration in tougher areas. For example, if you light a bomb and die before it explodes, whatever you tried to blow up will be destroyed after you respawn. Additionally, Skyward Sword "remembers" your latest activity, so you don't have to redo anything that's not unlocking a door or opening a chest. Not to mention, you won't restart all the way back at the entrance.
Finally, whenever you turn the game back on, you're where you left off in Skyward Sword. That's not necessarily true in Ocarina of Time, which often places you back at the Temple of Time or your hut in Kokiri Village, hindering your progress.
Beacons and Dowsing
This relates to the previous map section, but the ability to set beacons can be a life-saver in the different missions of Skyward Sword. If you didn't know your way around in Ocarina of Time, couriering that Odd Mushroom from the Lost Woods to the witch in Kakariko Village in under three minutes could have been problematic, especially without Epona to rely on. A custom-placed beacon would have been helpful.
Dowsing, while arguably overused in Skyward Sword, can be an extremely effective tool for finding secrets and finishing quests. I wish Ocarina of Time was nearly as good at guiding me to my next objective.
Quick Travel
Freeing Epona was a proud moment, but players went through a lot of trouble to get something that doesn't even matter to the game overall. Link's Loftwing in Skyward Sword might not be as personable as Epona, but at least flying is integral to the gameplay and story. You're also given a quick travel system almost immediately, which is a step up from having to waste time running around Hyrule on foot. And did we mention Link can sprint now?
I'm also a fan of the dozens of shortcuts the game places in the forest and other locales. The ones in Ocarina of Time barely deserved to be called shortcuts, considering you had to bumble through the Lost Woods (key word being "lost") to reach them.
Graphics and Music
Okay, let me stop you before you make your retort. I know, I know: The graphics in Skyward Sword have their problems. The game would look amazing in HD rather than blotchy and washed out SD, but it's still colorful. Ocarina of Time has those magical moments of color, too, but Skyward Sword is beautiful everywhere, while Ocarina of Time makes me wince every time I walk into Hyrule town in the past (or future, for that matter). I mean, the color scheme! Bleh!
Music has played an integral role in many Zelda games, and Ocarina of Time uses songs in interesting, dynamic ways. Skyward Sword does the same with the Goddess Harp (except you don't have to fiddle, err, ocarina, with a dozen different songs), but it's the background music that really stands out here. Did you notice that in the Bazaar, a different variation on the shop theme plays near each vendor's stall? How about those musical notes every time you swipe your sword at an enemy? A lot of creativity went into the score and sound effects in Skyward Sword, and it goes a lot deeper than "Zelda's Lullaby" played backwards.
Breaking Pots
I could name a lot of things for this last reason: like how the day/night cycle is less intrusive, hints are better and more negotiable, enemy design is slightly smarter and more varied, etc. But I wanted to talk about pots. I hate breaking pots in Ocarina of Time. Half the time I clang my sword off the wall and don't even break the pot on the second or third try. It's ridiculous! I don't even want those stupid rupees that much.
But breaking them in Skyward Sword? Easy as killing those tiny scorpions. And that's how it should be.
