Cloud, Sephiroth and numerous other FFVII characters may not stand out as much contemporarily in media, but what they all carry is the distinction of being at the top of their archetypes, thanks to being one of the firsts. So while they may not be unique by any means and may even seem like "just another of X" (like Cloud, a spiky haired anime protag with a huge sword) that's really thanks to them setting up the path of their distinctive genres.
I know for myself, if I didn't grow up in the 90s playing FFVII as my first FF and also getting into anime at around the same time, I probably wouldn't be as attached to the game at large. However, it worked out that way and it all sort of branches out that way.
Zack is uniquely interesting to me because he is an interesting and well-done traditional hero in an amoral and non-traditional world/story. Zack's heroism, good nature and kindness is ironically, punished and the root of most of his suffering. He's like a happy JRPG hero (like Sora) trapped in a cruel, gritty fictional world. The subversion creates numerous tragic outcomes.
Zack's pride and loyalty to SOLDIER and Shinra leads him to eventually getting experimented on for four years and then killed.
Zack's heroism and kindness leads to him diverting from his true mission of getting away from Shinra, choosing to try and save Genesis. He succeeds but that was vital time he lost. He carries Cloud around the globe, protecting him. His loyalty to his best friend and adherence to heroic ideals leads to him going down in a hail of gunfire. He protects Cloud and allows him to pick up the sword to be a hero at the cost of his life.
Zack's hopes and dreams are given to Cloud, and in a sick twist of fate, Cloud forgets him due to the experiments done to him. Thankfully he remembers, but for awhile, Zack is lost to those close to him. No one knows what happened to him and where he is. His parents don't even know his fate, to this day.
Zack is ultimately a dream. A dream of a hero which only exists now in the past because the world of FFVII fucking destroyed him. He couldn't live and fulfill his dream but it passed on and inspired those who could carry it out, like Cloud. He passed that legacy on and that's the only proof of existence that remains. Which speaks to how the world of FFVII is, it's cruel, harsh and unforgiving. But at the very least, Zack didn't remain forgotten.
To me, intellectually I sort of know why Cloud is the better protagonist, I understand that he's more complicated, but in my heart I just love Zack more.
It might have something to do with not seeing the real Cloud for 90% of FFVII. For most of FFVII, Clouds a bit of a douche, sure, we know it's not his fault (and honestly, it's not even as bad as me and many others imagine it), but it's still what I'm stuck with.
And even knowing this, I am still stuck playing as "a puppet" to some extent, while I sympathize on an emotional level with boyhood Cloud and his guilt, fear of failure, etc. None of that is something he seems to be actively going through in the original game.
He has those issues yeah, but the point is that he's repressing those issues underneath a Soldier persona, while that's great storytelling, it does mean I don't actively see him struggle with those issues. The issues aren't revealed until the lifestream sequence, but that's also the point where those issues are mostly resolved (if we don't count AC for a second).
The thing we actually see Cloud struggling with is his identity crisis, which is interesting, but is experienced by us as mostly an actual tangible issue, not an internal issue. We don't really see Cloud struggling internally with actual character flaws, those underlie the fake identity, yes, but he's repressed them, he's unaware of them, or at least pretending to be. So it's presented as an actual external thread, something Sephiroth is doing to him, rather than an internal one, which is where characters get their humanity from.
So I, like Aerith, don't really know Cloud, which is why I find it hard to love him, because I don't see him for the first part, and by the times we get him back there is no longer any time, or need, to really watch him work through it.
I think I WOULD have liked Cloud more than Zack, if I had had an entire game of him during, and post, lifestream, where I actually see him grow the way I saw Zack grow.