I only played Secret of Mana once, just the begining; while Super Mario RPG I played almost completely, but it was a long time ago so I don't remember very well -.-
From what I remember, Secret of Mana is an action-RPG, while Super Mario RPG is turn-based, isn't it? Super Mario RPG is very, very good (when I first played it I though it would suck, but it's actually an excelent RPG) - the battle system is very good, quite creative; the story is very funny and interesting, and the graphics are good for the SNES. From what I remember, the difficulty was quite well adjusted (not too easy, not too hard), and you won't get bored easily.