Both to be honest. They both really work on Zelda games. It's just sometimes one or the other works more closely with one game while other person takes notes. They have both sort of put something into most Zelda games wether Aonuma has been in charge while Miyamoto supervises like they have been doing. Not going to vote who is better because it sounds silly imo. Both great people.

I just get very happy when I see someone say the Wind Waker is their favorite Zelda game..

It's not that simple is it? Doesn't Miyamoto play some kind of supervisory role in some respect even now? 

Actually, Majora's Mask damaged the franchise in terms of sales and deflated hype in the series. Wind Waker represents somewhat of a recovery in sales compared to Majora's Mask.

I wasn't that much of a Twilight Princess, but who knows, maybe you'll like it more than I did! Skyward Sword, however, is a Zelda game you should definitely play! The story and soundtrack are easily the franchise's best if you ask me!

Miyamoto obviously. No contest.
Even the new Zelda for Wii U is taking as a base the first masterpiece Zelda NES.

I'm sorry, but if you're saying the fate of the Legend Of Zelda series depends on whether it looks like this:

or this

Then maybe the series just needs to die, because to me it's just ridiculous. The series has (for the vast majority of it's life) been based in a multiverse, and people can't accept a little change? I love the fact that few zelda's look the same yet feel like they deliver the same core experience of a series. It's why Zelda is still one of the freshest game series even today. 

Beyond that, I don't know if the Zelda series could survive being a series with every iteration having a realistic art style. Major studios that use this philosophy are closing down, bought out, or in risk of one or the two. Could this reflect what would happen to Zelda? No, because Nintendo isn't just a game dev, nor is it solely dependant on one system or game series. They got money, and a major financial hit wouldn't really amount to much. However, the ends have to justify the means, and the cost of development would be far greater than the money gained from another mill or two being sold. And that's even if the Wii U would be able to handle a vast open World with realistic graphics in the first place. I'll take a cel shaded Zelda that surpasses Skyrim, then something that looks practically exactly like Skyrim but has better frame rate. 

With the cel shaded style we don't have to sacrifice anything. We get small details rendered very well, we get great looking textures, we get a good lighting system and particle effects, ect. I see absolutely nothing that looks half assed, and that excites me.

I agree that artstyle has been a constant disscusion regarding maturity, but mechanics are more the cause of the split fanbase.

We went from ALTTP 3D throught 3 day mechanic, sailing, wolf, to motion controls. Now we are back to open world, as the first one.

Definitely Miyamoto, it's not even close. He designed The Legend of Zelda, Zelda II, ALttP and OoT. All masterpieces.

Since then we have titles like WW, TP and SS, as well as ALBW. All of Aonuma's titles have been simply building on the OoT formula, or more recently a re-imagining of ALttP. Very little progress and I would argue regression. He introduced the divisive topic of "Artstyle" being an actual thing to discuss. His titles will seldom be heard in discussions of "greatest game of all time", unlike the Miyamoto titles which almost all heard such talk upon release.

The brightest hope for Aonuma Zelda is Zelda U, and this is again not because he is coming up with great ideas, but because he is drawing inspiration from the original incredible game Miyamoto designed so long ago.

I think Aonuma is also responsible for the stupid split timeline thing because they had to fit in the moment of insanity that was WW. Under Miyamoto I'm pretty sure it was just:

OoT->ALttP->Zelda->Zelda II

Also, for those bringing up Majora's Mask, that was the brainchild of Yoshiaki Koizumi. He was a key part of that game design (story, 3-day concept) before leaving to lead his own team.

Thank you for bringing that up and giving him credit. Him and Miyamoto made that story what it is today.