What about Final Fantasy Mystic Quest?
Then there was Secret of Evermore, which was made by Squaresoft of America, but the "real" Japanese Squaresoft had nothing to do with... Then there was the remake of Capcom's Breath of Fire that didn't get very favorable reviews in GamePro magazine... I didn't actually play those last two...
When Secret of Mana was new I didn't get very far because I failed to level up my magic periodically. When I revisited the game as an adult I learned this was necessary to complete the game.
Anyway... Secret of Mana was a good game. Very underrated soundtrack, just great music.