Chrono Trigger > Secret of Mana Plot is more developed, intensive, and interactive. Character's have back story and display emotions. Techs offer unique skills for each character Multiple...
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Chrono Trigger > Secret of Mana
Plot is more developed, intensive, and interactive. Character's have back story and display emotions. Techs offer unique skills for each character Multiple endings increase replay value
Secret of Mana > Chrono Trigger
Weapons and spell development adds length and strategy Classic
OVERALL
Both of these games are great, however Chrono Trigger is definately the better of the two.