I would say the first difference is that you notice is FoE has much more of story arc, CoC is more explore unlock. Then CoC has a far greater range of possible pairings (to the extent that it sometimes feels a little "Gotta catch them All"), where as FoE's much smaller cast tends to be more subtly shaded.
CoC is the pioneer and sometimes the scars of development show, FoE was created with the lessons of CoC in mind hence its code is deliberately kept clean.
FoE probably caters for a wider range of sexual identies