While it may just be a fan effort, I think Zelda: Clockwork Empire is a mix of interesting ideas and flawed ones as well. Where it gets it right conceptually, it nails it but it also seems to undermine a lot of who Zelda and Link are just to make Zelda the lead protagonist.
The thing about that is much of it just isn't necessary. Zelda doesn't need to be a commoner, Link doesn't need to be a prince and the less common ground they have in terms of fighting abilities and origins, the better.
Let's start with the basics of the Zelda canon - and there's going to be some Skyward Sword stuff here so if you've still not played it, you may wish to click back now. Before I get to the SS stuff, though, we all know Link, Zelda and Ganon are part of a fated cycle. For years Nintendo just made up history as they went along with the Zelda series, but we know these characters were fated to be reborn over and over and repeat the cycle even without Skyward Sword's extra details.
So we now know from Skyward Sword that Ganondorf and various other evils that may plague the land of Hyrule come from the reincarnations of the evil god, Demise. We also come to learn that the one that originally sealed Demise away was the Goddess Hylia, but that her power was spent in doing so and she was later reborn in mortal form as Zelda, Zelda goes off on a pilgrimage with Impa to awaken some of her latent power and gains a great deal of wisdom along her journey. Link became her protector and went through many trials to prove his courage and forge the Master Sword. Demise wishes only for power, subjugation and destruction of the weak.
Its here we see Link and Zelda purge the evil with the magic of light and the Master Sword. Later their reincarnations are bound even more deeply to fate as the Triforce breaks apart and Link, Zelda and Ganondorf literally become avatars for Courage, Wisdom and Power during the events of Ocarina of Time. This is an important theme to keep in mind when approaching these characters. Each of them is part of a rather conflicted whole.
Clockwork Empire does its best to acknowledge Zelda's alignment with magic and wisdom. From her magic gauntlet to her family's links to the Sheikah Tribe, this fan work hits most of the right notes in how Nintendo could tailor a game to the character of Zelda. The use of magic, stealth and acrobatics aren't really Link's best strengths, so emphasizing them for Zelda and building a game around such skills is a great way to set her apart and in how The Legend of Zelda could be played
But give her the Master Sword and you're already undermining her qualities and stealing Link's alignment to courage in the process. That's a big problem. Wisdom defines Zelda, courage defines Link. This is just the way the series is written and going against it leads to poor writing and lots of other contrived ways to make Zelda a Female Link rather than Zelda as a protagonist.
Also contrived is Clockwork Empire's desire to make her a commoner. Zelda is often portrayed as royalty and while its true this has not always been the case - as Wind Waker and Skyward Sword prove - she's always been a natural leader whether she's a schoolmaster's daughter or pirate captain. Simply put, a Zelda without that sort of station and commanding presence just isn't Zelda. Again, there are exceptions to this - like her cowardly, selfish and ghostly incarnation in Spirit Tracks - but on the whole Zelda is a respected and collected leader.
But just because she has such a high station as princess doesn't mean she can't sneak away from the castle as herself or in disguise to have some adventurous fun. If Brave's Princess Merida can sneak off off to shoot arrows, ride her horse and go rock climbing - why can't Zelda?
There's plenty of rebellious, headstrong princesses in fiction. I'd actually like to see a Zelda that, while noble and wise, was also a bit headstrong. I think there's something inspiring about a royal that fights out of a genuine love for her people and doesn't give a damn how she's perceived for doing things considered below her station if the disguises fail or she's caught in the act by nobles and knights.
With this in mind, I'd like to keep Zelda and Link as they've always been. In fact, one of my favorite interpretations of the characters is having them be friends since childhood, which both Skyward Sword and The Minish Cap draw upon. Why can't the princess just be the friend of the local blacksmith's nephew? This again shows Zelda is about more than her status as a princess, that she truly loves her kingdom, friends and probably better understands the weight of her status than she lets on. I would even say her greatest fear is to not be able to live that way and be unable to protect her people. An evil could rise that preys on her worst fears just after she started to get a bit more bold.
And if Link's games start with courage and he gains wisdom along his journey to vanquish evil alongside Zelda, shouldn't Zelda's adventure start from wisdom and her journey be about overcoming fear and gaining courage to vanquish evil alongside Link? As Sheik, Zelda would give Link wisdom and a song to aid him on his quest during Ocarina of Time, why not give Link the chance to pass along some of his courage to Zelda before he's kidnapped and Hyrule Town is attacked?
I think these are really the things we should be starting with. Additionally, since Link goes through a trail to get the Master Sword - a trial that proves courage - why not have Zelda set out on a quest and trial to test her wisdom and obtain a sacred bow of some sort? Zelda has often taken to using the bow and light arrows - or just light magic - while helping Link seal away Ganon. I think focusing on the bow as a weapon is also another opportunity to give a game led by Zelda a different feel and style of play from that of Link's. I'm actually quite keen on the idea of Zelda being a stealth action character that uses magic and Shiekah arts to misdirect and terrorize enemies as she picks them off at a distance with a bow or crossbow.
Nintendo did once say they toyed with the idea of Zelda as a shooter and I think ranged weapons and magic are natural skills to Zelda. Having these along with stealth, magic and acrobatic platforming would naturally play into the puzzle solving and boss battles the series is known and loved for.
I'm not saying she has to strictly be about the bow and magic, either, as Twilight Princess does set a precedent for her making some use of a sword. I just think the sword would be best as a secondary weapon, a means of parrying attacks since she wouldn't have a shield - and that's distinction Clockwork Empire also makes regarding her.
Finally, since Light Arrows have commonly been dispensed to Link near the and of many games and the bow and light arrows are later taken over by Zelda in the final confrontation, it stands to reason Zelda - having gained much courage on her journey - could prove worthy of the Master Sword before it later gets handed over to its destined wielder, Link. The whole light arrow thing being left in the last or near-last dungeon has always been James Bond villain-level dumb, but grabbing up the Master Sword in the last or near last dungeon would stand to reason given the franchise's history.
So have a game that plays on what we know to be true of the Zelda character, build it around her unique skill set - emphasize magic, stealth, acrobatics and the bow lahead of swordplay. Make her about ranged combat, put her evasive and athletic skills to work. From there, give her all the usual tools - the bombs, hookshots, boomerangs and such - that she would need to solve puzzles and hurt or stun opponents. Tools are an area that can be exploited by both characters as it wouldn't really feel like a Zelda game without them - though I suppose they could devise some new tools to use exclusive to Zelda.
That aside, what we don't need a Zelda that's just Female Link. Its not inspiring or empowering - its just borrowing Link's role and that's boring. Its also pandering to radical feminists rather than creating a good female character. Zelda deserves better than that and so do her fans, so give a her a story where she can express her own strengths, her wisdom and rise to overcome fear, Give us an inside look as her life as a royal, the ability to sneak away from it and live among the citizens of Hyrule. Let us see the world from her eyes, the thrills she enjoys being away from the castle, her friendships among the citizens and her desire to protect them with her life.
I think that's really the Zelda we deserve to see and if Nintendo were to make such a game, it wouldn't have to be the last time Zelda was cast in such a role. Make her a Female Link, however, and I promise you her adventure will simply be a one-off. I don't think anyone wants a one-off.