Here's my input and let me say it's totally my opinion from an FX owners perspective, so take it as that. Don't want it to become a food fight and I'm trying to be as impartial as possible:
FX:
The good = very light/strong, very nimble, slight nose/tail rocker built it, entire hull is glass (not SMC), very dry hood design.
The bad = small pump (122mm vs 144mm), only made in '94 and '95 so hard to find. Less stable for peeps wanting an easier platform.
SJ:
The good = 144mm pump, more availability of aftermarket parts, very stable/easy to ride, gobs of steering ratio (on pre-'08).
The bad - Heavier (~ 30lbs), SMC hull (bottom deck), hood design seems to take on a lot of water.