I love seeing Star Ocean 2 getting some attention! And the deep relationship system is one if its best-realized, unique-or-close-to-it traits. I wrote about it a bit in one of my own articles [http://www.pixelpoppers.com/2009/09/play-me-story-part-two-what-makes.html], using it as an example of consequential choice that allows a player to steer the story.
To me, it's one of the most disappointing things about the followups (Till the End of Time and The Last Hope - I never played the Japan-only Blue Sphere) that the relationship system got so drastically reduced, and the pair-anyone-you-want endings vanished. It's still satisfying to immerse yourself in the characters (I also wrote about The Last Hope in another article [http://www.pixelpoppers.com/2010/02/giving-in-to-happy-place-embracing.html], as an example of... well, a game where it's satisfying to immerse yourself in the characters) but some of the magic is definitely gone.
I wonder how much of this is due to raised production costs. In A Second Story, endings were new text with pre-existing sprites, backgrounds, and music. It wouldn't be that expensive to write more and more. In the later-generation followups, with full voice-acting, recording all those endings would cost significantly more, and they'd take up a lot more room on the disc, too. It's one of the biggest downsides of increased production values that they reduce this kind of flexibility.