You might want to try the Ogre Battle/Tactics Ogre series. Those games are pretty long, have deep stories, have multiple endings, and allow to customize your characters and teams to an extent.
The Ogre Battle games, Ogre Battle (SNES, PS1) and Ogre Battle 64 (N64) play like a combination of a RTS game and a traditional rpg.
The Tactics Ogre games, Let Us Cling Together (PS1) and Knight of Lodis(GBA) play much like Final Fantasy Tactics. In fact the same guys who made the Tactics Ogre/Ogre Battle series also made FFT and FFTA and are currently making FFXII.
Another recommendation is Star Ocean: Second Story on the PS1. It supposedly has 80 different endings and the characters are very customizeable.