Best ones are already mentioned, but... Golden Sun, StarCraft and Zelda: OoT.
I haven't played any games that comes even close to the amount of character building and story telling as these games. Then again, I haven't played many of those classical SNES RPGs either.

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Haven't played Golden Sun a lot, but I remember a huge rock crushing my town.
Starcraft was interesting.
As for OoT, it's terrible. I say this because the plot is VERY SIMILAR to A Link to the Past. You have the six sages which translates to the six maidens in LttP. There are two versions of the same world just like LttP. Finally, you have to fight... dun dun dun Ganondorf!
If it was original, it would be okay, but that would be given to LttP. It's more of a copy, though they switched a couple things.
I'd say MM would have the most original plot for a Zelda game.