I think Squall is a great leader of the party, but just not a great protagonist. I don't he progresses enough for anyone to really gain any kind of sympathy for him in any way. I remember playing the game for the first time, and towards the end, I felt as indifferent to Squall as a character as I did in the beginning of my playthrough, and that is not what I'd like to experience when I play the game.

I think Zidane is the best protagonist of the entire series. He may not be the best leader, but he is certainly the most likeable and the easiest to gain attachments to.