As you emphasize the storyline, it depends as to whether you prefer a sci-fi adventure (Star Ocean), or religious and philosophical content (like in Xenogears) or a less serious quest (like in most RPGs). You can't go wrong with any of the games you listed (let me point out that Suikoden III has a very good plot with an original perspective, if you're interested, and Dark Cloud 2 - also known as Dark Chronicle - has many charismatic characters, but none of these games are from Square or Enix).