Okay, this is a long one, so hopefully I can bring some of the points accross. Also, it's good to know that the game doesn't necessarily have an explanation for everything, similarly to RT, where there is no explanation on why certain things happen - it's often not important to me how it comes about, but what the consequences are. Okay, deep breath and...
>>> Is there any reason Ochi developed the Ori personality in the first place?
No. It's not explained.
>>> Why does the eye operation lock her into Ochi mode?
Not explained. Anesthetics can easily affect your brain... a combination of factors... anything.
>>> And Ochi's lamentation that Ori didn't come to see her...she can't possibly have ever laid eyes on Ori since they're the same person...so....what?
Well, they were switching day by day, and they knew about each other, but they couldn't put the pieces together - it was an explanation that seemed logical to both of her personalities. At the times when the game had a section that explained the illness in more detail, there was also mentioning of Ori and Ochi going into therapy, so it could also imply that referring to one another as sister was the best ordered therapy at that time.
>>> How does Ori resurface in ending #5?
The ending is also partly residual. There is a slight hint at this, almost untraceable... in a not included scene Yoshiyuki is at the hospital and they consider the effects of the shock if someone would speak determinedly to Ochi, implying she is Ori - and Ochi would be in a highly unstable state (i.e. her aggressive fits), and if she wouldn't see the one who was speaking and so on. It turned out to be a complicated explanation and so I decided to drop it. But Yoshiyuki makes the same telephone experiment... he even AFAIK mentioned that it should "work".
>>> Why do Ori and Ochi merge in ending #4?
Becaue Yuki is born, but no explanation beyond that. Hormone levels, but I didn't want to crete wild theories. The non-biological explanation is that a baby is the symbol of ultimate love - both mental and physical - that's why it brings the split parts of love together. (see below for a bit more detail on the split.)
>>> It strikes me as kinda strange that that's the "best ending" since it always seems to hinge on Yoshiyuki recognizing that he loves Ochi's body...that's the best thing for their relationship?
Yes... actually the good endings are Yoshiyuki going with the body - he would probably have known Ochi's baby wish... in fact that's why it's so important to have deciphered Words Of Melody. It tells you the wish, and all that there should be to do is submit to that wish and make love... when the time is right. (yes, when the time is right... *hint*)
>>> More importantly, how does Ori differ from Ochi? I feel that’s something of a problem, actually... We don’t get to see Ori do all that much, and she isn’t much of a character...
That's because she has no real role. She is merely a personality that carries only love - therefore when he is with Ori, Yoshiyuki feels love - while with Ochi he can feel everything else (especially physical attraction). It's in fact just a device to put Yoshiyuki into a situation and see what one can live with - especially the question would be can you live with someone on the grounds of physical attraction?
>>> I know mikey said he was focusing on one character, but given that Yoshiyuki was in love with her, and, as it turns out, she's the same person as Ochi, there's an odd lack of infomation on her.
The focus was to show what a person would be if the ability to being loved or feeling love from someone would be taken away from her - Ochi was a comparably normal personality (though still a bit on the possessive side, but still, nothing out of the ordinary). With the split, Ori was "born" and she took everything love-related from her life. Ochi was left with everything BUT love in her life - that meant she was increasingly evil and irritated, frustrated and so...
Of course, when Yoshiyuki came into the picture, he fell in love with Ori, as that was the part of the personality that could give, but also receive love. Even though nothing else happened, barely any physical contact or anything else... Yoshiyuki was in love. But before he could realize that beyond love there's really nothing more to Ori (which would result in a similarly frustrating problem) ... the operation came and there was only Ochi left. And being confronted with Ochi to whom he could feel attraction (sexual), he decided to stay with her, as it was the same physical person as Ori. It could have been clear to him that the lack of love in their relationship would inevitably lead to problems, but it was the (newly found) physical attraction (as a sort of second side to love), that gave him hope and the will to be with her. At that time though, he didn't realize that he felt love for Ori and attraction for Ochi - both felt in their way somehow right - but neither of them alone could be enough to make him truly happy - and he found that out by living with Ochi, the one he was attracted to. He says in 4/9 that he probably would have the same unfulfilled life with Ori as well when he finally realizes it.
>>> The same is true of Onoe, really. She’s irrelevant to the main plot of the game, even though she was Ori’s friend. Doesn't she have anything to say to Yoshiyuki about her?
Not really. She isn't really involved, as she was friends with the non-conflict love-only Ori personality. And in many ways Ochi/Ori is competition for her. She likes Yoshiyuki and she does not hide it. And she is also a different personality altogether - as Yoshiyuki is more a submissive personality, Onoe is the only one who he can have an equal relationship with, her love makes him drop the submissive tendency he had. In this respect she is not relevant, as the story of Yoshiyki and Onoe's relationship, if it had to be detailed, would probably be a very different story.
>>> Wait, didn’t the game say in Part 0 Onoe and Ori were friends since kindergarten? Didn’t ending #4 say that the Ori personality didn’t emerge until later? She was born Ochi, right?
Yes, she was born Ochi Ryokawa, the normal, if a bit dominant-by-nature Ochi. Onoe knew her at that time and they were friends. Now... later on, Ori (she represents love) was separated from Ochi, and now there were Ori and Ochi (the aggressive). And Onoe stayed friends with Ori, and wanted to help her. She also had much more tolerance for the Ori-Yoshiyuki relationship, even though she wanted Yoshiuki as well, than she had for Ochi when Yoshiuki and Ochi became a couple after the eyes operation. She was still not resigning, but she didn't take any action or didn't want to make Ochi look bad, even though Ochi had that aggressive nature and was treating Yoshiyuki like that time in the office. Yoshiyuki, if he wanted, Onoe would love him at any time - in her ending it says she loves him unconditionally, a different sort of love - and Yoshiyuki also says he needs this kind of love, which is kind of true if he wants to have an equal relationship.
Well, hopefully it could clarify a few things.