I think this goes back to more than just Yuga as far as the problems surrounding the main antagonist. I would argue that, other than Ganon/Ganondorf, no other antagonist has really made much of an impact on the players simply because they haven't been given much of a backstory or have had much ambition different from Ganon himself. Take Demise for example: We know that he is seemingly the original evil which plagued Hyrule (or the "world" in general) who was later resurrected as Ganondorf, then Ganondorf (or Ganon in most cases) was himself resurrected multiple times. So other than what Ganon had already established in prior games which Demise would come to be given some credit for as he was the original incarnation, his backstory was relatively weak. He was just there in a sense, much like Maladus in Spirit Tracks, although to a much lesser degree. Maladus had even less of a backstory other than being an evil that was sealed away by the power of the Spirit Tracks. He had a very strong resemblance to Ganondorf and could have easily been made out to be a new incarnation of Ganon (or Demise if you want to argue that, though that story had yet to be written), yet he was not even given this storyline to sort of tie him to the rest of the series in a siginificant way.
Yuga is much the same in that he was simply another bad guy from another world who bore some resemblance to Ganondorf, or the Gerudo tribe in general, and acted as Ganondorf himself would have in the same situation in that he captured Zelda, the Maidens (or Sages in some cases), and all-around rose hell throughout Hyule. Even though Ganon was brought into the story, arguably in a weird and perhaps even unnecessary way, it didn't do much for Yuga's character other than perhaps belittle it by saying he needed the essence of Ganon to do something he was already doing. Maybe if Yuga had been designed differently, with a different look, maybe then he would have been a better villain. But I think moreso than general design, the main antagonist needs to separate themselves from previous villains in a more significant way than their name.
What we have here, at least in my eyes, is a play on the same old story for the antagonist (kidnap Zelda and attempt to rule Hyrule or the world), which is much like the same old story of a young boy who appears as if out of nowhere, clothed in the same tunic of each legendary hero before him, in order to thwart whichever evil is plaguing the land. The difference is that while the hero himself can keep this same story and everything be fine, which has pretty much been the case all these years, the antagonist cannot keep this same story and remain interesting. The hero is, after all, supposidly the "player themselves" and therefore a backstory for Link is not overly important, just as the backstory for Zelda herself is not important as she is merely the Princess of Hyrule and needs to be nothing more. But for us players, we want our antagonist to be, not only menacing, but interesting enough to truly feel their menace. And this does not have to take two or three games to achieve; Remember, Ganon didn't have much of a backstory at all until ALttP, and even then that backstory wasn't truly fleshed out until OoT. Even Majora's Mask itself was a villain who was just ate-up with backstory, feels, and so much tyranny that you felt it in one game, and the player didn't even really know until the end that the Mask itself had a conscious of its own and was not merely a voodoo-esque tool.
I think Nintendo is playing it a little too safe these days. They don't want to flesh-out a new backstory for a villain because they either feel like it needs to be nothing more than the simplistic "steal the princess, rule the world", or perhaps they feel like straying from this at this day-and-age might confuse or alienate new players. At the same time, they don't want to keep reusing Ganon over-and-over for much of the same reason. They essentially create a new villain and give them the same goal or ambition as the previous one.
While I have loved Eiji Aonuma's work over the years and will continue to support him as long as he is doing his thing, I can say that the only thing that will fix this issue is a new set of writers and a more emphasized focus on the story of the Zelda series. We know Nintendo likes to focus on gameplay first, and that's fine; That's how it should be... But the story, especially of a series so deeply rooted in Nintendo's history and one of the biggest bread-winners the company has, should be just as important.
