An Under rated SNES game that I found and enjoyed is Live-A-Live, an Japanese only title made by Squaresoft(before it became SquareEnix) which came out in 1994, the same year for FF3/6 came out, which is mixture of a RPG/Strat. game with its battle system(one of the most unique RPG battle systems for the SNES, in which you move in a grid and have to choose where to be at on the grid to have your attacks to come out, and also how to avoid getting hit by your enemies.
The story has eight different story arcs to it, with stories like: A caveman saving his woman, kung fu master trying to find a worthy pupil, ninja trying to assassinate a emporor, two cowboys trying to save a town from bandits, an cyberpunk mecha story, an wrestling trying to become the best in the world, 2001 a space odyssey type story, and a story tying all it all together.
It never came out in english, but there is a fan translation patch that translated all the game into english, but I do believe there are minor translation errors for what I know. So, if you want to play it, you would need to find a copy of the game, dump the rom, and apply the patch to play it.
Also there is are a couple downside to the game, the graphic suck on it(It was the same year that FF3/6 came out) and it shows that they didn't put enough time with the graphics at all, and some of the stories are not that good for the arcs, and the battle system is very weird to get uses to at first. Also, you WILL need a guide for it because the translation messed up some parts of the game, so you won't be able to figure how to advance without one, just letting you know.
But, it has some amazing stuff to it, the battle system is the most amazing thing I have seen in a SNES RPG game, and some of the story arcs are amazing, and the ninja assassin story arc is amazing, with you can fight every single enemy in the story or try an Metal Gear Solid approach to it and avoid killing as much enemies as possible to it, and make the game more of a challenge because you will low level trying to beat the final boss in the story so, you can make a challenge mode for that story.
Also, it has some amazing boss music that I love:
https://www.youtube.com/watch?v=p1Nmc84Noos
Live-A-Live is an amazing under rated title!