Both are spectacular games and it really isn't fair to say one is better than the other. That's like trying to compare two sunsets or something cheesy like that; they're both wonderful.
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And just to play the game, I think FFVI is the better game of the two. While Chrono Trigger did have good character development, an crapload of options for the player to go down, great music, great story, and great gameplay, FFVI beats it on all of those except gameplay (actually, FFVI has terrible gameplay).
The character development in FFVI is just unmatched and that's the thing that matters to me here. All the characters just change fantastically and even the villains change. In the time before the internet the twist on the floating island was unheard of. The game was one of the very early console games to deal with suicide and death. The music was topnotch and still has some of the most recognizable themes today. The story is classic. The game has quite possible the best villain ever.
The list just goes on. Both are great games and it's unfair to call one better than the other (that's like saying the loser of the Superbowl sucks) but I would have to say FFVI is better.
