Personal interpretation bullshit all of this.
It's my headcannon that Cloud is irrefutably bi or sexually confused after his potential skimp out at Honey Bee Inn and the schizophrenic nature of his brain under Jenova's influence is what makes the early him so indecisive. Sexually, mentally, romantically and as a person. I don't remember but I think Jenova was messing around with his head in that place, too.
All the characters have issues which tie them back to their identity. When Cid was forced to choose between his dream and Shera's life, he was in fact choosing between exploring his aspirations as a pilot and being human. Barret's custody issues and the farce of being Marlene's father. Cait Sith explains his by existing.
Perhaps, all of these are about accepting everything in you and being a person. Humanity, nature wins over all of them. They were all, in some way or another affected by Shinra - the Shinra who are ubiquitous with, an anthropomorphication of, corruption and dehumanization. Of forged identity. Genetic splicing.
There's an interesting book called simulacra and simulation, by a french philosopher. I prattle on about this one a lot but it talks about a world dominated primarily by symbolic representations of real things rather than those real things themselves. Maps instead of the area, brands instead of quality, language categorizing and manipulating feelings, the disconnect between money and what it represents... It's most readily apparent in, how, you could be as talented and knowledgable as someone who has completed a major for that subject field, but you need the corresponding piece of paper to be readily acknowledged as such by the simulation we live in. That simulacra is what you need.
(Oh god, that actually sounds like Cloud... He wasn't a SOLDIER by definition.)
FFVII might juxtapose a similar dilemma, with Midgar's rampant industrialisation and monopoly over Gaia. It's a world that, as with ours, violently oppresses any alternatives. Since the infrastructure of our world might end up causing it to hit a landslide at train speed by removing the brakes, invalidating democratic consentus and keeping as many of us in the dark as is possible... It's not too far from reality.
Edit: Also, I've always seen Sephiroth as a product of humanities' ignorance as well as all the other things he stands for. Shinra catalyzed him via their usual morbid desire for convenience at the expense of safety, and without such a reckless trespass of the unknown there might have been no way anyone would harness active Jenova cells. Sephiroth is a freak. A complete bastardisation and perversion of nature, a symbolic representation of going too far and ruining everything.
Although I do like the image in my head.
