I think the more "emo" portrayal of protagonists in Final Fantasy have more to do with how society views its men than you people give credit. Back in the days when Final Fantasy III was first developed and released, which was April 27, 1990 (and thus the development was earlier than that), the majority of gamers were men, and men of the time mostly didn't care for "emo"-type characters; if you looked at mainstream entertainment icons from the time when the game was developed, they were all fairly masculine with a defined way of how a man should be.
However, as time progressed, the way society perceived men began to shift; Final Fantasy VII, which was released on January 31, 1997, was released during a period when women were beginning to impress upon men how important being "sensitive" was; hence, Cloud and Squall both have quite an "emo" quality to them, which have only gotten worse as perceived gender roles and political correctness continued to change towards what it has become today.
This is probably why many of the male players prefer "manly" characters from the franchise such as Final Fantasy VII's Cid, Final Fantasy VIII's Seifer, or Final Fantasy X's Auron; those characters weren't particularly communicative of their emotions and gave off a more "gruff" masculine demeanor. In many ways, male gamers look to video game characters for attributes they themselves wish they had, and thusly, those characters who display stronger masculine traits tend to gain more favor with male games than those who show more "sensitivity".
Personally, I'm not really a big fan of Seifer myself, although I must admit I'm quite partial to Auron (hence my avatar) and found Cid more interesting than Cloud, but not by much; from Final Fantasy VIII, though, I prefer Zell, who I thought was a better example of "well-adjusted" than any other male playable character in the game.