The article makes baseless assumptions such as this: "Look at A Link to the Past and Ocarina of Time, for instance. It would be a disservice to the former to call it lesser simply because it's not a 3D adventure. It is a fully-realized 2D masterpiece, and only serves to illustrate the differences between the two types of games."
I think most people prefer Ocarina of Time because it really did take the series to another level, and not solely because it was 3D - but in the end, Ocarina of Time managed to be a game that was as fun (if not more fun), and also significantly more satisfying due to the more lively feel of Hyrule, the many additions, and greater excellence in game design among many other factors. It was genuinely a better game.
Ocarina of Time is also not really any more difficult to understand than Link to the Past, it is a highly intuitive game. The difference between 3D Mario and 2D Mario is that the 3D Mario games are really a different genre, you change the core gameplay around... This core mechanic change does not exist in 3D Zelda, the transition was in fact straightforward - it served to change the player`s perspective, and allow for more detailed gameplay (look at the boomerang).
Link to the Past is a phenominal game, for the time, but it wasn`t very long before there were games out that arguably exceeded it: including Enix`s Illusion of Time and Terranigma, and Matrix`s Allundra. There are a great many people today, nearly 15 years later, who consider Ocarina of Time to still be the best game ever made.
Ocarina of Time doesn`t take anything away from Link to the Past, but there are a number of very good reasons why it is considered with higher regard than Link to the Past, and not really any good reasons I can see why it wouldn`t be. It has nothing to do with the simple fact that it is 3D and the other is 2D, there is a great deal more reasons why it is considered the superior.
I personally don`t think a 2D Zelda would be very exciting, not like a 2D Mario. 2D Mario is a different genre, 2D Zelda is the same genre with limitations. If anything, I do think that the Zelda series needs to move forwards and not backwards. There are a great number of options available: Make something like Terranigma, a Link who rebuilds the world; or even a Sandbox Adventure title - a genre which is popular on Xbox 360 and PS3, but hasn`t really been explored on a Nintendo home console - so it doesn`t have the same saturation level that those platforms have (With Sandbox Adventures like GTA, and Sandbox RPGs like Elder Scrolls). If Nintendo made a 2D Zelda, there would be an IGN article complaining about how blatantly Nintendo milks their franchises.
I describe myself as a little dose of toxic masculinity.
