I really think that the issue of Sephiroth's origin and feelings becomes a lot more clear if you pay close attention to the subject of the Projects in Crisis Core. In which they said that Angeal and Genesis were created as the first experiment, as well as many others, but were ultimately deemed failures because the resulting body was unable to retain its form and would eventually break down (in such a way that it is clearly different from a normal human having to die and then decompose). And during the course of the game, their bodies do exactly that. But I recall, during the discussion between Angeal and his "father" (However that actually works out, parents in FF7 seem very complicated) a certain piece being mentioned about Sephiroth. That he was the result of a newer project, one to create the perfect soldier or weapon, and to make amends for the weaknesses in the earlier experiments. Sephiroth's creation was, as he put it, "perfect." It's probably a good thing he wasn't present for this discussion as I imagine the trauma would have been even greater.
Sephiroth was a toy, an organic plaything, an experiment, and his life meant practically nothing, yet he had feelings due to the way he was raised and the people he knew. Yes, his malice and barbaric strength, overpowering anyone, is clearly obvious in his spar with Genesis, if you can call it that. How much he knew of his origin is questionable, since he obviously knew there was something specific to him that was abnormal, otherwise he would not have offered to help with Genesis' healing, which was not so much aimed at the cut on his shoulder, but that Sephiroth had overheard something about the "degrading" process of their bodies. The idea that he must be something different must have crossed his mind. The reason for his grouping with Genesis and Angeal had to have crossed his mind, but I imagine he suppressed it, for the same reasons why we suppress the obvious signs that lead us into curiosity.
But furthermore, Genesis and Angeal were still around when Sephiroth went haywire. A lot of people see the Nibelheim incident and seclude it only to meaning Sephiroth, Zack, Cloud, maybe Tifa, and the topic of Jenova and the Ancients, because the Nibelheim incident in FF7 only showed that. Whereas in the real version, not a recollection of Cloud's, was that Sephiroth had Genesis and Angeal on his mind, their betrayal, what Shinra was actually up to, where he fit in, and at the same time, he had the misfortune of being partnered with perhaps the most unlucky of all the final fantasy heroes. If Zack had only managed to say one dumb thing in his life, I think the phrase "Normal members of Soldier? You mean you're somehow different?" had to be the one. At this point he realizes that he is no different from his two counterparts. And not only that, but one memory Cloud never recalls, because he wasn't there, is that Genesis visited Sephiroth RIGHT after his revelation. He blatantly tells him that he should join Genesis and help him find a cure for his degradation. That they are brothers and are struggling together. I'm not quite sure how that was supposed to tempt Sephiroth, because he just says I hope you rot, basically. But surely the information he seeks in the Shinra Mansion goes much further beyond that of just his origin and Jenova and the Ancients. The unfortunate part of both games is that he only reads an excerpt of alllllll the books he intends to study while he's down there. And that excerpt is mostly tailored to the facts of the original game. Whereas I'm sure he read much more than that, such as the origin of his two "friends" and how they were different, the purpose of the experiments in the first place. The conclusion he came to was simply that of all the experiments that were presented, as they were written (which some say are false, although it's possible the books were butchered, or the scientists were just not right before they died), is that he is a product of a so-called Ancient and that somehow this experiment was deemed perfect and they used its results in further development of SOLDIER members.
Whatever it was that made him what he is, he soon realized was not a product of the Ancients, and it also existed in numerous other beings, and him being the first, the perfect result, he was purely of this "Jenova" essence, which had survived for centuries. His will, his being, as it exists in the lifestream after his initial death, is the same as Aerith's. The difference is that, whatever properties this Jenova essence contains, allows him to remanifest himself in numerous different ways. For instance, in the original FF7, the Sephiroth that resurfaces and stalks Cloud and his gang, leading him on, is often referred to as a Jenova manifestation with Sephiroth's appearance. The Jenova monsters are simply not expected to look like him. The Sephiroth forms at the end of the game, are also Jenova manifestations. The Sephiroth event directly after is considered to be the metaphorical deathstrike, erasing Sephiroth's grasp over the lifestream, but in the end, it simply hadn't done so, as Sephiroth seemed to imply in Advent Children. I do not think his final words, "I won't exist as anyone's memory" or however it was stated, were entirely poetic. He has resurfaced through his manipulation of the life stream already plenty of times, and without somehow tampering with the lifestream itself, it will be impossible to stop him from continuing so. So in this sense, I don't see any true contradictions. By the time he kills Aerith, he already knows better than to try and indoctrinate her, she is as much the enemy as the normal humans are, and poses an even greater threat at the moment. Otherwise I don't imagine he would have gone out of his way to assassinate her and no one else.
The things I can't seem to gather any real facts for are where Gast/Hojo fit in, since from CC to the original FF7 (the middle) I don't see any information to piece them into the puzzle, and what exactly Kadaj and the others are... or where they are from. As I watched the movie, I seemed to get the feeling that they were the same as the Sephiroth "Clones" from the original game, they said something about having.. developed, that's what gave me that feeling. And that Kadaj was the most developed of the three, therefor he was somehow closest to Sephiroth, and felt him in his soul or something along those lines. Otherwise I'd say that they're simply weak Jenova recreations that had somehow been left out, or created during a weakened stage of Sephiroth's will, in which pure Jenova cells were required to strengthen it. I'm not sure, that seems pretty foggy to me. This is the reason why I have always considered FF7 to be the best, simply because no matter how many times I play it or watch it, there's always more questions. But for the topic of this thread, guess I should summarize: I don't really see a lot of contradictions between the series. Aside from a few personality differences that can be explained through the presence or lacking of voice actors and maybe some names changing, which I'm hoping is what happened with Gast, since he seemed to disappear.. It's mostly a lack of information in some places that I would like to have. I know this thread is old, but I had been reading over this subject a lot and decided to post my opinions here. My apologies for the rant.
