Yes, after all the various plot epiphanies I've experienced in the last few weeks, I've decided that I'm going rework a few significant points of COI's plot.
Whew. That being said, fortunately, the changes are going to be pretty much limited to one character -- namely, Dr. Savois. And why, you might ask?
It's because I want to hurt Zack badly and I can't really do that with the current Savois setup.
Oh dear. That sounds terribly sadistic of me, doesn't it? O_o
Well, to be honest, I've been bugged by the... well, inequity... of suffering between Zack and Cloud in Nibelheim for a long time. Cloud's experiences make hell seem like a dream vacation but Zack pretty much just gets locked up like a zoo animal. Big friggin' whoop.
So making Zack's experience in Nibelheim much intense makes things a bit more 'fair', so to speak. Besides, it means more possibilities for Sephiroth-angst, which is generally a good thing, yes? After all, Sephiroth does a horrible thing to protect Zack from Shinra and Hojo, but ironically ends up serving Zack up to the tender mercies of Hojo and his ilk on a silver platter for five years.
I'm not saying that I'm going to make Zack's Nibelheim experience as bad as Cloud's. That would be pretty hard to do, actually. But Zack's time in Nibelheim will still be pretty damn ugly. After all, Hojo will want answers about the whole Sephiroth debacle and you can bet that Zack won't be cooperative. Can you say 'interrogation scenes'? Yes, I knew you could. :D Zack, being a mentally and emotionally stronger person, handles it extremely well, but there WILL be some long-term consequences of the more subtle sort.
How does the creative freedom to make Zack suffer more relate to Savois' character? Well, if you go by the original COI plot, she loves Zack, so it's damn hard to rationalize why she would just leave Zack at Nibelheim for five years if he was being seriously tortured, especially when she knows pretty much everything that's going on there. It's not impossible to explain, of course, but personally, I find it a very difficult sell.
However, if I remove her romantic interest in Zack and change her schemes/motivations so they center around researching the various dispersed Cetra genes floating around the human population, and how they interact with Jenova cells, that simplifies matters considerably. It also provides a plausible reason why she's so interested with Cloud and now with Rufus. ^_- It will also help make her more mysterious so it's not so obvious what her overall goals are. She can still be very helpful to Cloud and Company, but she's now a significantly more ambiguous character because of her secret agenda.
The Super-SOLDIER program and the Cetra genes are related because it's a specific set of Cetra genes (shared by Cloud and Rufus) that make the Super-SOLDIER program even feasible. Those Cetra genes are why Rufus can tolerate high intensity mako exposure without turning into a monster. And yes, Rufus can also be transformed into a 2nd Gen SOLDIER... theoretically speaking, of course. ::evil grin::
After thousands of years of interbreeding, most humans have at least an odd Cetra gene or two. Most of the time those Cetra genes don't have any noticable effect or are dormant. However, certain people who have especially potent complexes of Cetra genes (e.g., Cloud and Rufus). Sephiroth himself probably has a different set of Cetra genes which interact uniquely with mako and Jenova-CORE cells (otherwise, he wouldn't have survived to birth). Zack has yet another different set of Cetra genes. And so on.
::sigh:: Who knows, given how new COI-plotbunnies keep popping up, this might not be the last retcon I find myself doing.
But don't worry. I was already planning a major rewrite of COI (i.e., COI Redux). I'll incorporate the retcon stuff into the Redux version and leave the original COI chapters alone. However, be warned -- Chapter 8 and on will be based on the revised COI Redux version, so there WILL be some plot inconsistencies with Chapters 1-7.