If a true novel was released then I doubt you'd be submarining to this cave anyway 
You would use a Chocobo for it, of course.
According to Vincent's flashbacks, Lucrecia's "vision" in her cave (what/where exactly is that cave - it looks really odd?), and Hojo's own words at the end of the Disc 2 assault on Midgar, Hojo created Sephiroth by injecting Lucrecia - who was pregnant with his child - with Jenova cells.
As Dan said it everything is about will power. An embryo has no will after all*, but the gift of a soul from the planet (you could say it's some kind of not living yet). Maybe they hoped to create a pure minded Cetra this way.
Sephiroth clones made post-Sephiroth - especially the Nibelheim clones made in the wake of Sephiroth's rampage in that town - are made by injecting people with Jenova cells and showering them in Mako energy/radiation (I think radiation is a better term for it than energy). This is the exact same procedure used to make members of SOLDIER, differing perhaps only in intensity and duration.
The thing is, that Hojo used the victims of the Nibleheim incident - we do not know if the people were dead or only deadly injured, but I guess the first thing is the right. They have a soul but no mind anymore and this is were they are equal to an embryo. So Hojo used the body's to recreate Sephiroth alike persons but only to proof his reunion theories, not to create super strong soldiers. These persons will join Jenova one way or another like Sephiroth did in Nibleheim.
However these persons didn't build an own (fake) personality like Sephiroth did and stayed brainless. Cloud is an exception, maybe he wasn't dead like the others and his (weak?) will was something which was needed for a successful 're-production'. This could make sense according to Hojo's statement that he thought Cloud is a failure. He didn't thought that Cloud would be become a good copy, because his will would resist to Jenova. That's why Cloud has no number.
*Apparently this was one of the wrong conclusions of the science team.
The game is very vague to these things. Maybe one reason is that the Dev's have written the story alongside they have developed the game.
- Had you thought about the truth of the mysteries regarding Cloud and Zack from the very beginning?
Nojima: No, I thought of it as I went on with my work. So at the beginning there wasn’t much foreshadowing. The foreshadowing scenes, I asked the staff in charge of the event scenes to add after development reached a point where an outcome for the mysteries came into sight.
Kitase: In those days it was easy to go back and change things around later on. Lately, with the workload involved in making the graphics, it’s hard to ask people to change something once it’s been finished.
Nojima: Well, even back then, there were some people you could easily ask to change an event later on, and people who were difficult to ask, so the locations of the foreshadowing might be biased. I only went to the people who were easy to ask, and the foreshadowing is focused at the scenes they were in charge of (laughs).
http://thelifestream.net/lifestream-projects/translations/2693/ffvii-10th-anniversary-discussion-p-8-to-13-of-the-ffvii-10th-anniversary-ultimania/
