Before we get started on our FFVIII playthrough in the next couple of days, let's just go ahead and "clear the air," shall we? Since I'm sure this will probably be the most debated game of this series. Well, maybe XIII, since I actually like the game.
I'm going to keep tabs on the "Signs that Squall actually likes Rinoa before we get to Disc 3." Some people will say I'm reading too much into things, but to me, there are enough of them that they can't all be pure coincidence. You can rule that out if you want to, but that's just my take on it. Most of those signs are deliberate.
But then you have these people who will say, "Yeah, but a lot of those are choices you make! You can pick all of the bad choices, and then what happens on Disc 3 makes no sense!" To that, I must also respectfully disagree, and I'll explain why. For most of those choices, you are picking what Squall says/does outwardly, not what he thinks inwardly. Repeatedly throughout FFVIII, we see that what Squall says or does on the outside is not indicative of what he thinks or feels on the inside.
Let me explain what I mean. For Squall, his goal is complete independence. Anyone who tries to get in the way of that, he reacts against it. Probably the best non-Rinoa example is Quistis trying to talk to Squall in the Secret Place. That's probably one of Squall's biggest "jerk" moments in the game, but is it really as simple as "Squall's being a jerk and he doesn't like Quistis?" I don't think so. Throughout the rest of the game, Squall shows a great deal of respect for Quistis as a SeeD. He selects her to lead the Gateway Team at the end of Disc 1, for instance.
So what was the issue? Well, the obvious issue is that Quistis is trying to intrude on Squall's independence and make her way into his personal life. As a result, Squall resists and does everything he can to push her away, and he succeeds. Squall and Quistis's relationship is pretty civil from that point forward because Quistis really makes no more attempts to get into his world. The difference between Quistis and Rinoa is that when Squall puts up resistance, Quistis relents and Rinoa pushes back.
In reality, Squall's not really a jerk who hates life and hates everyone around him (which is a common misconception and what causes a lot of people to label him as "emo" or whatever you want to call it). He's fine with being perceived that way, as he divulges on Disc 3, because it keeps people away from him. The main reason he avoids relationships isn't because he hates people. In fact, it's quite the opposite. It's because he realizes how easily he gets attached to people and how close he can get to them that makes him want to avoid those relationships, because one day, those relationships end, and all you're left with is pain and emptiness.
So now you may be asking, "What does this have to do with picking all of the bad options for Rinoa again?" Simply put, Squall being a jerk to Rinoa on the outside doesn't mean he doesn't like her and doesn't care about her. In fact, it may convey just the opposite. He's afraid of getting close to her and may in fact be aware of his budding feelings for her and her feelings for him, so he tries very hard to push her away before those feelings can bear fruit. Of course, once Rinoa's life seems to be in potential danger, Squall can't run from those feelings anymore and everything rushes to the surface. He can't keep them inside anymore as he faces the possibility of losing her, and so we have Disc 3.
That being said, this is all just my personal take on the matter. You are free to disagree. I just think "But you can pick bad options and it makes the story make no sense!" is a little oversimplified and potentially offbase.
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SuperNiceDog followed this simple flowchart to win the Guru!
http://img600.imageshack.us/img600/8718/leonflowchart.png