FC2's setting, sound (remember the thump of the 50cal?) and general believablilty were superior to FC3. What I mean by believability is that you played as a veteran-turned-merc instead of some playboy-turned-rambo who is miraculously able to dominate both a pirate and a mercenary organization with no training whatsoever. Even if FC2's main lacked personality (due to the breadth of choice I'd imagine) he/she was still a far superior protagonist than Jason Brody on the grounds of believability alone.
That said, FC2 wasn't fun to play where as FC3 was. The issue with the AI shooting, accurately, through ten meters of jungle, which you can't even flippin' see through, was intensely irritating. That factor alone was enough to make the game a "once-through" for me. Just about everything was fine if not great.