It's a pretty difficult question to answer since everyone's experiences are different and it's all open to interpretation, especially with the different translations. One person can consider Magus the most complex by picking and choosing the best lines from Woolsey, DS, and the unofficial translation, and his involvement in Radical Dreamers (and utunnels' trans of that) but it can easily be argued he's incredibly 2-dimensional if you stick to one game, one translation, and just what is presented to the player, withholding what WE project onto the characters.
The best default answer would probably be Crono, who is meant to be an avatar for the player, but you can't ignore the impact his/your death had in the game. It can be interpreted as the character being insignificant, or as a thematic device to show the entire team's/humanity's/YOUR insignificance in the face of death. All open to interpretation.
Then there's characters that seem to leave the story exactly how they entered it. They don't change or develop, you just find out more things about their core character as they go through the adventure. That doesn't make them flat, but they still qualify for the answer.
In the end I think the characters in this game were meant to be painted with very broad strokes so that we as players can fill in the details ourselves, even if we misinterpret a lot of actions.
Also I'm super glad Marle hasn't been everyone's answer so far yaaaaaaaay