Chrono Trigger 
Secret of Mana Overall Comparison 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 valueSecret of Mana > Chrono Trigger
Weapons and spell development adds length and strategy
ClassicOVERALL
Both of these games are great, however Chrono Trigger is definately the better of the two.
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Comments
ive played neither of those games. probably should play them at some point.
I have played both of these games multiple times through, maxed out all characters, got every single ending. I enjoy Secret of Mana much more, I have to say. I can agree that the story and multiple endings for Chrono Trigger are a big plus, but, I never felt bored of the combat system in SoM, and that is a must for me. I get tired of waiting for the 30 seconds that Luminaire takes to finish.
ta
The active system of SoM was great but if you’re a completionist like me than leveling up all of the weapons and spells gets awfully tedious. Especially towards the end when you have undine spells that pretty much dominate over anything new that you received due to use.
Agreed on the Luminaire, it should have been an option to at least skip some of that cast time.