Way back in the chuunin finals (see chapter 113 or episode 66-67) Kakashi remarked that the reason he'd trained Sasuke was because he was "the same type as me". He says this at the same time Sasuke revealed that he'd learned Chidori. Then later it's Kakashi who explains what chakra elements are to Naruto and mentions that he's got a lightning affinity. One might draw from these two events that Sasuke's natural affinity is also lightning. If that is the case it could be part of the reason for Sasuke's initial difficulties with learning the Fireball Technique since learning to manipulate your natural element is supposed to be the easiest.
From what Yamato said most of the Uchiha were Fire types but if Sasuke wasn't then it makes sense that he would have had a harder time learning Fire jutsu than other Uchiha members.
But it's also possible that Kishi just makes everything up with absolutely no thoughts given to plot consistency in which case Sasuke's elemental affinity must be fire because he used fire techniques first and because if someone says most x's are y then it really means that all x's are y.
@Abdula: Where are you getting lightning > fire from? The 'circle' of strengths and weaknesses doesn't seem to have any meaning for non adjacent elements. According to the chart Fire should be neutral compared to Lightning and Earth and Lightning neutral compared to Fire and Water.