In my own humble opinion, the all-time greatest "old school" RPG and perhaps the greatest
SNES game period is
Square's Chrono Trigger!
There are have been other RPGs with epic stories that include numerous surprising twists and affords multiple alternate endings, side quests, extra playable characters, etc--but I'm hard pressed to think of another game that spans so many multiple disparate chronological eras, thereby blending together several sub-genres within the broader fantasy and science-fiction umbrella, and incorporates powerful, novel, and down-right fun cause-and-effect time travel scenarios! It's practically
Doctor Who: The RPG!
Moreover,
Chrono Trigger had a fantastically varied combat system that allowed your party to grow together and not separately, learning special character specific team-work moves!
(And, yet, despite my absolute love for
Chrono Trigger as professed above: its sequel
Chrono Cross completely passed me by! (Its release just so happened to coincide with a time in my life when I put aside gaming for a few years to concentrate on my studies, etc!) I'm definitely going to have to make of point of playing it at some point! Retro Gamer Bucket List updated!)