I personally think the series shines the most in games that do not feature a plot that involves Ganondorf or the Triforce. For example, Majora's Mask and Link's awakening have been heralded as the high points of the series on the main console and the handheld. The freedom to create an entirely new story, free from the constraints of a traditional Triforce-centered plot does the series a major service in terms of creating fresh, unique experiences.
I think the mistake Skyward Sword made was to set up a character as well written as Ghirahim, with a flowing, constantly evolving character and personality, and then to "Zant" him suddenly somewhat at the end of the game for a completely new, unfamiliar villain that we otherwise didn't know or care about. Ghirahim was perfectly capable of killing Link - his [sadistic] charm was that due to his self-importance, he felt he was genuinely above Link, and felt obliged to restrain from killing him due to what one can interpret as a recognition that Link was a "lower life-form" that wasn't worth the time. Ghirahim is a far more formidable and sadistic villain than Ganondorf.
People generally (and largely) cite WW Ganondorf as sa great villain - but I feel this is because he was far better written as a tragic and borderline-byronic anti-hero.
It was the quality of the writing and characerization of the character that made him so well received - not the fact that he was Ganondorf.
In fact, to give a sort of valid credence to this, people often criticize
TP for its clumsy writing, and very much disliked how Ganondorf was crudely jutted in at the end in a "surprise" moment and felt he was an unnecessary and irritating addition, prefering Zant as a new villain, before it was revealed Ganondorf was suddenly on the scene.
I think Nintendo first and foremost needs to refine its story writing and characterization. Which characters are then used in the game is secondary to this.
Ganon was also present in the cd-i games, but his appearance did not in any way mean that his appearance was an indication of good quality.
I think however, Nintendo are more acutely aware of their faults - especially their handling of
TP, and are learning form it, if
SS is anything to go by.
I'd personally love a game of the child Ganondorf, living the life as he described in WW, growing up in poverty, witnessing his tribe die around him, and become more enraged and jealous of the affluence of the Hylians, slowly turning him into a vengeful spirit who wanted to usurp and control everything the Hylians denied him and his tribe. Because other than WW, Ganondorf has largely been a one-dimensional villain that really doesn't add anything to the stories of the games, other to infuriate fans when he's suddenly included as a last-minute boss in a game that doesn't really need him as a character to function, or be told well.