I just can't seem to decide. I really want to play the game with 3D on seeing as how I own a 3DS and all I would want to use that capability. However my eyes started hurting a bit after a few hours of play, and I turned off the 3D. With the screen at it's full resolution, I gotta say the game looks fantastic in 2D. With 3D the screen is split resolution-wise and while the game still looks great, there are noticeably quite a few more jaggies or aliasing, which is something us PC gamers strive to avoid. Thankfully in 2D, the jaggies disappear and the retextured (I'm noticing they retextured a ton of stuff) surfaces looks crisp and clean.

Now I am horribly torn on which way I want to play through the game and was curious to see what you guys were falling on.

Edit: So far after some more fiddling around, I am starting to move towards 2D. I've noticed the framerate is a little more stable, but that is seriously me being super nitpicky. Overall the more I switch back and forth, the more I notice the 3D isn't super substantial, although there are some cool effects here and there, like all the fairy shit or whatever floating around Kokiri Village.

Been trying both with and without. First time for me playing a 3DS game so I wouldn't know if this is a good or bad implementation of the 3D, but I could see the gimmicky part of it all. I prefer the 2D, so does my eyes.

I'd be totally cool with playing this gaming without 3D. It feels like it doesn't really fit to be a 3D game, at least to me. I'd rather enjoy it just for the awesome game it is, not for the 3D effect.

I've been playing it for about 3 hours now with 3D on (tried switching it off a few times to see the difference) and I must say I love it.
The added depth to Kakariko Village is amazing. To me it is the best way to play the game (so far, though I might change my mind if i run into trouble down the road).
That being said, I have found a few instances (the conversation with Zelda in the Castle courtyard comes to mind) where I had to turn the 3D down just a little bit to be able to focus on the characters, but that was the only time.
As for now I'm all for 3D on the 3DS (have also enjoyed some Ghost Recon on the console which has a much more subtle 3D effect to it).
 
I think Nintendo's new console is great, and playing OoT on it just makes it better. And if 3D poses problems for the eyes, the game still looks good in 2D, but I for one will attempt to play through the whole thing with 3D on.

I really like the 3d, it looks like the entire world has depth in the 3DS. I like to keep it on, I just wish my eyes were better/more tolerant for it.

Wait, the resolution is actually lower in 3D mode? Or do you mean that jaggies just stand out more in 3D mode? I don't have this game yet, but in my experience with the 3DS, the 3D mode looks way sharper (but also duller colors), even when looking at 2D images (such as the backgrounds in the 3DS store).

No, the resolution is the same (400x240 on the top screen). When running in 3D mode it produces an 800x240 image, 2 x 400x240 images effectively that are almost the same, one for each eye.
Meaning the actuel game-content-image-thingy you are looking at is the same resolution whether it is 3D or 2D.
The frame rate is a different matter though. I haven't noticed any difference in Zelda but I've read that Street Fighter is 60fps in 2D and 30fps in 3D. Which is logical because the actual screen size that needs to be rendered in 2D is half of what is required for the 3D equivalent.
@MrKlorox:
Didn't see your edit about jaggies :) Yes, I've noticed this aswell. When I switch to 2D the image seems more aliased. It would appear that viewing it in 3D has the added bonus of a slight amount of anti-aliasing (whether this is intended or not is another matter).
 
Re-reading you post makes my above comment seem like nonsense :) anyway. I experienced the exact opposite. I think the image seems more detailed (not less so) in 3D compared to 2D.

I play in 3d though the first heart container i collected nearly burst my eyeballs and there is the occasional ghosting on the screen but adjusting the slider helps

@AdmiralBobbery said:

When I switch to 2D the image seems more aliased. It would appear that viewing it in 3D has the added bonus of a slight amount of anti-aliasing (whether this is intended or not is another matter)

Really? I get the exact opposite. I get a smoother image in 2D and 3D it is sharper but more aliasing.

Am I seeing this backwards or something? I can't help but feel like 2D has a better visual quality about it overall.

I turn it on, but not full, usually less than half way to avoid it hurting my eyes. I cant really comment on the resolution, but i do switch back and forth, and i dont really notice a difference. I like the little touches 3D makes, for example, when in Kakariko Village, grabbing those Cuccos, the feathers pop out through the screen. That being said, the game doesnt need 3D to function. I really hope one day a game will be made that actually benefits on the 3D.

Well, I don't have a 3DS, but I'm starting to want to go back and boot up my N64 for another shot at beating Ocarina of Time. So, I'm going to be playing it in what was considered 3D back then, and what I still call 3D since I don't really talk about Super 3D enough to make the switch to calling games "polygonal".

@AdmiralBobbery said:

@wolf_blitzer85: This is weird :). I might just be me being new to the whole 3D gaming thing. Still got a layer of fairy dust over my eyes. I will experiment a bit more with it when I get home from work

A good place to switch between 3D and 2D to see what I'm talking about is the overhead scene after the drawbridge before you enter the town square. Between each mode it looks like the difference between 1x and 2x AA to me. Weird stuff man.

i cant see 3d so... yeah... :/

Will check it out later today and post my findings :)

I've been switching back and forth. 3D tends to hurt my eyes if I look at it for too long.. but the game does look really amazing in 3D, especially the big scenes where you get the master sword and stuff like that.

one thing i noticed is how much clearer links chest belt is with the 3d turned off 

Screwed up the last post, so let me try this again:

I think the smoothness effect is because you can't see in-between the pixels as easily as you can when in 3D. Less of a "screen-door effect".

But AdmiralBobbery is also correct with his point about the 3D making it seem anti-aliased. The slightest variation in perspective will give you a different image that won't line up perfectly on top of the other one, meaning the differences will be blended (unless you've got an overly dominant eye), which is pretty much how MSAA works.

Then again, anything's plausible with a game from Nintendo. It might actually use better assets or another resolution when in 2D to burn those extra frames. Who knows?

@AdmiralBobbery said:

@wolf_blitzer85: This is weird :). I might just be me being new to the whole 3D gaming thing. Still got a layer of fairy dust over my eyes. I will experiment a bit more with it when I get home from work

A good place to switch between 3D and 2D to see what I'm talking about is the overhead scene after the drawbridge before you enter the town square. Between each mode it looks like the difference between 1x and 2x AA to me. Weird stuff man.

It looks pretty damn cool in 3D, but I usually just turn it on to look around and then shut it off.

I've been leaving the 3D on the entire time with only a few exceptions. I do turn it off when the camera angle gets bad or during the occasional boss fight. I've noticed that when a wall or item or character model is right up against the edge of the camera, the 3D looks way too weird for those bits and ruins the rest of the effect (try walking down a hallway, pushing up against one wall, you might see what I'm talking about as the walls passes the edge of the screen). In those cases, I turn it off. And the giant Octorok miniboss fight, I had to turn the 3D off because the camera just wasn't playing nice with me and that made the 3D effect look kind of awful.

Aside from those cases, I play with the 3D turned on and the slider all the way up. I think it looks fantastic and I manage to slide right into the 3D's sweet spot almost immediately.

I really like playing it in 3D.

This seems to be the question about 3DS. 3D or not 3D? The answer is simple. 
With 3D, you get, well, 3D effects. 
Without 3D, you get better framerate, and better anti-aliasing. 

I like playing in 3D because, well, it is a 3DS after all, and this game makes fantastic use of it. But yesterday I turned the 3D off to get a little bit more battery life and I was pretty impressed with the 2D mode. Aside from the antialiasing that has already been discussed, the screen with 3D turned on shines in a weird way and looks kind of "glassy" you have to see it for yourself to understand it, it is not noticeable until you turn the 3D off and the screen looks like a normal screen. It's like when you don't notice the annoying noise of an air conditioner until it turns off.

On for cutscenes and off for gameplay.

Been playing it with and without the 3D. I like both but imo you just need to turn the slider up just a bit to get a good experience.

Can't see 3D on that thing. Not much of a choice for me.

Off as much as it seems like a cool idea id rather play OoT on a handheld, with or without 3d doesn't matter.

Been sticking with 2D like I have been with the other 3DS games.  Sure it does look neat, but it  just kills the battery if you use it.

3D is really well implemented and I like it but the game doesn't really call for it. If I'm near a charger I turn it on for funsies but if I'm not I play in 2D to conserve battery life.

The 3d adds a lot to the look of the game, but it definitely does tire the eyes. So far I've either been fully on or off - I might try it with the slider at around halfway or so for my next play session and see what that does.

One neat thing I found is that if you want to use motion controls for aiming with 3d on, closing one eye (like you're actually aiming) negates the breaking of the 3d effect enough to make minor adjustments. Using motion to aim is a really neat and useful addition, probably moreso than the 3d in my mind.

I really like the 3D-effect, I have the slider just slightly on and that's just enough for me to be satisfied. Awesome game.

OoT 3D is one of the only games that I can comfortably play with the 3D slider all the way up. Most games I have it around half-way.

I''ve been switching back and forth so far and probably will continue to but it will be less and less on 3D.

On 2D the anti-aliasing makes the environments looks so much better doesn't seem to do as much to Link thought. Its especially when the camera flies around (like when you enter a new area). The framerate seems fine in 3D but i haven't done any comparison.

My biggest issue with the 3D is the double image that at first only seemed to be happening to Link but now seems to be happening to lots of stuff even parts of the environments. At first I thought i was just moving the 3DS too much in my hands but whenever it happens now i've tried closing one eye which then causes you to only see one screen and there is no doubt about it that there is a ghostly second rendering of Link. This feel like a huge bug to me and a even bigger oversight for Nintendo for letting in go into the final product.

LIGHTSABER ON!!!!!!!!!!!!!!!!!!!!!!!!

I think the 3D looks amazing. It's how I play it 95% of the time, while the other 5% is when I'm laying in bed.

The 3D is awesome and i use it all the time!

I bounce between the two.  I will usually play in 3D until my eyes get tired and flick it off.  Typically I turn it back on when I get to the boss chamber.

The 3D's gorgeous. I don't like the 2D, it looks blurry to me.

And wow at people still having the slider either all the way up or off, you're doing it wrong.

It looks pretty good most of the time in 3D so I usually keep it on but in some places I get a lot of double images or ghosting I guess it's called. Mostly have to turn it off when the camera is too close in on link or during some cutscenes. The worst is in the first sacred realm scene with the golden fountains (when you become adult link for the first time; I could see the fountains and then a ghost fountain to either side of each one, I had to turn it off for that cutscene. Just general running around is fine though but it does seem to be worse as adult link for some reason...

Haven't tried 3D much I'll admit, maybe I will more during Master Quest.

I've enjoyed the 3D effect for the most part. I have noticed my eyes getting tired pretty quickly. I blame part of that on the constant ghosting I see at random points in the game. The worst so far has been any of the tunnels you crawl through. I've been hitting the switch to 2D more than I would want from a game and system that touts the 3D angle pretty hard. Still enjoying playing OoT again though.

@GunslingerPanda said:

And wow at people still having the slider either all the way up or off, you're doing it wrong.

Wut? To my eyes, all the way up on Ocarina looks fine. And I'm sure some folk are absolutely fine with it turned off. You condescending twat.