Both Pathfinder and FantasyCraft have their roots in D&D (as does Spycraft, honestly). A lot of the basic rules are similar, but FantasyCraft has, in my opinion, diverged the most. I find FantasyCraft to be more rule-detailed than Pathfinder, so is more suited to groups that like more structure. Both games are fairly combat-oriented, but FantasyCraft offers a better (in my opinion) mechanism for handling social "combat"
Finally, there seems to be a LOT more support for Pathfinder than FantasyCraft. That can be a benefit for groups that don't have a lot of spare time.