[Zutroy]

MGS 3 does have a great storyline and is overall one of the best games I've played. If you don't mind going old school, and if you can find a copy, Suikoden 2 had one of the best storylines I've seen in a game. It was very compelling and didn't really lose steam as they tend to. Suikoden 3 also had a great and uniquely told story in it. Those are the only two I've played so far but I think the Suikoden series is pretty grossly underrated. Anyway, both are worth looking into if you like the FF series.

Also, I didn't see this mentioned but Grim Fandango is hands down a must-play if you are looking for story. The graphics are quite outdated but I think it is still playable. Adventure might not be your thing, but it is seriously worth considering (again it is rather old so tracking down a copy might be difficult).