So I'm about 2 years late, but here's my opinion. Both games are fantastic as we all know, but each have their pros and cons. Skyward Sword being an up to date game of course distributing a wider variety of things like mini games, color, graphics, new techniques, all of that. Although that's an unfair advantage, it's there. Also, SS presented a much more hype affect when battling, especially in the final boss(holy shit, that was a fun battle). Hell, even fighting the Imprisoned got my heart rate going. Also, was I the only one that was given anxiety when doing things in the Silent Realm? Jesus. As for Ocarina of Time, I'm sure we all love that game not only due to great gameplay but due to nostalgia and sentimentality. Ocarina of Time featured more standout memorable moments in the context of the entire series than any other game before and after it. Everything from galloping through Hyrule Field for the first time with Epona, to the powerful opening screen that was based off this image, to entering the Temple of Time for the first time with that simple church hymn in the background that made the place feel important, to pulling the Master Sword out from the pedestal and most significantly (in my opinion), two of the most memorable experiences in the entire series; the ascend up Ganon's Castle amongst dozens of flights of stairs with that ominous organ music getting louder as you drew closer to Ganondorf only to have purple energy inflicted onto Link from Ganondorfs gauntlets and then the descend down to the base of Ganon's Castle when the Castle was collapsing following successful completion of the first phase of the final boss.
It's honestly hard to choose, but I'll have to go with Ocarina of Time being better, although Skyward Sword is right there with it.