I don't know why I didn't realize it was a poll when posting before.
I said Magus originally but now, after thinking, my vote ties Crono and Robo for 2nd place behind Magus as site fave, as of this moment...
Crono's an interesting take on the rpg protagonist, if you think about it. They usually use western-style swords by default, in FF games and DQ. But Crono doesn't pick up a broadsword the whole time you're playing, that's Frog's thing.
I guess part of it was how complex they were making the animations, and making two people use the same weapons seemed like a waste of space on the ROM. You notice that characters have far more specialized weaponry in CT: Each character can only use one type of weapon.
Magus is #1 because, I think, there is something interesting about someone who could give two craps if the whole world thinks he's the embodiment of evil, so long as he gets revenge on the space bug that destroyed his entire family and nation. That's some high-grade dedication and conviction.
He is a villain who deserves a chance to be a hero, and that's not usually how they play anti-heroes.