The difference is, Zidane had a personality and Squall didn't. Which makes it more believeable that someone would eventually love him.

Zidane was into Garnet from the beginning and he slowly won her over. The princess and the loveable rogue is nothing new, but for a video game it was pretty well done. Squall, on the other hand, was emotionless, cold, and distant for the majority of the game and then all of a sudden he was into Rinoa, a girl who liked him back for whatever reason (never really explained well from what I remember, but it was a long time ago). It really made no sense to me that they got together other than the fact that it was the whole theme of the game.

Zidane+Garnet is to Squall+Rinoa what Han+Leia was to Anakin+Padme. One love story bloomed slowly out of circumstance and the other was forced upon us because that's what the plot dictated.