This is a bit off-topic, but Onikage, I think that for a team leader, I'd say Marle. She has the most ties to Crono and does have a bit of a leadership aspect. (being the royal heir and all) Lucca's good too, though.
(Janus definitely would not make a good leader personality-wise, I think... He strikes me as a loner who prefers to do things by himself, not really one who's good at leading...)
I agree about Magus 100%. When I used to put him in charge, it kinda felt like... well if you're a Dragon Ball fan, there's this part in the Cell Saga when Goku is put out of commission. Vegeta, despite being a jerk and loner, winds up with the crew following his lead just because he's the strongest protagonist on the field. Magus has good leadership capability, but he's a bit of an odd fit for the main group.
I've thought about Marle. She does seem to have the most motivation to save Crono, and is the de facto character to hang with him on the peak after. I just don't see her as a leader-type figure. I know she's a royal, but she kind of plays against that type during the game.
Ok, so I guess right now it's a tie for me between Lucca and Glenn. I say Glenn because, having lost Cyrus and then Crono, I could really see him spearheading the project to get back his best friend. Also, if you have him in your group when you recruit Magus, he shows the authority to send the others off. He also makes the choice to allow Magus into the group. Without him, it's a 3 person group effort. He really seems to come into his own and his old lack of confidence is gone.