Got to say that I agree with Garo more or less entirely; this list is made up things which aren't unique to Ocarina of Time and can mostly be found in almost every Zelda game. I also agree that Zelda U shouldn't take any specific lessons from Ocarina of Time because I feel, as Garo does, that Ocarina provides a basic framework for 3D Zelda and that the later games in the series have built upon it in interesting and creative ways to provide unique and imaginative gameplay experiences.
One thing I will say is that, while I would love for Zelda U to have a more involved villain, I personally would never have held Ocarina up as an example of that. The writer, in the actual article, comes up with three points in the story that involved Ganondorf and that was it. Considering that Ocarina of Time is (on your first go at least) about 30-40 hours long, perhaps longer, these individual moments are far spaced out with a lots of events taking place in between. And sure, Ganondorf might get mentioned from time to time outside of the examples given but that's no different to A Link to the Past when every dungeon ended with a speech about Ganon, or Skyward Sword whenever Ghirahim shows up and never fails to mention his master, Demise. I know the article asks for the "ultimate evil" to be more present but, personally, I'd be just as happy with Zelda U doing things similar to how Twilight Princess handled Zant. Zant was ever-present and got invovled a lot in the first half of the adventure, we were introduced to the idea that there was a higher power behind him early on but it was left vague and mysterious enough for us to not be certain this "God" will replace him, and his behaviour and actions change in the second half as Link defies him more and more, so we see the player's actions having an effect on him. Skyward Sword doesn't come close to this (for reasons I have gone over at length in past threads and so will not include here) but just because it didn't do it as well doesn't mean the villains were not just as present, arguably more so than in Twilight Princess. If you ask me, Zelda is on track with making the presence of its villains known and Ocarina of Time has nothing to do with it.