I can kind of understand what you are saying. The more superficial aspects of the game don't compare well to modern games for sure. However, I just never cared at all about graphics so this doesn't bother me at all. The controls could be better (the camera control in Wind Waker for instance was a noticeable improvement from Ocarina and Majora's Mask), but in this respect I think I really just became so used to them that it's hard for me to find fault with them. I personally would say that the game aged extremely well because I would focus on the core gameplay which I would say still beats the vast majority of games released today. There is no video game I have played more than Ocarina of Time, and there are plenty of video games that had beautiful graphics that I played once and never wanted to play again (L.A. Noire for example). I think it's fair to say that Ocarina of Time shows its age because its graphics are from 1998 and its controls are limited by the N64 controller, but that Ocarina of Time aged extremely well.
Continuing my example of L.A. Noire, Ocarina of Time is like a person that ages normally but makes good decisions when they are young, takes good care of themselves, and lives a long time. L.A. Noire is like a person that makes every bad decision possible, gets tons of plastic surgery to look good, and then dies young. I want to clarify that I don't even think L.A. Noire was a bad game, I just used it as an example because it's a game that is actually well-known for its graphics rather than gameplay. In other words, I think Ocarina of Time ages extremely well because its strength is gameplay and that is timeless. If you judge a game based on graphics, then very few games age well. No matter how much effort is put into making a video game look pretty, 5 years later it's obsolete looking with some exceptions (the only game I can think of is Wind Waker). Controls there isn't as much of a difference- pretty much since the Gamecube's generation there haven't been huge improvements in controls imo. Soon we may get to the point where games stop aging in terms of graphics though because there is only so much the human eye can perceive and graphics will keep improving by less and less each generation.