I finished with the good ending first, and after a day or so I was told that I missed out on some more content, so jumping back into an awesome game I already beat to discover a new plot twist and finale was extremely satisfying.
The build-up to final encounter and the mythology behind it drew me in too. Then there's that awesome theme music and "uphill fight" atmosphere going on that made the climax of the battle and game totally impressive. Low on supplies and MP, the last few turns were down to the wire for me.