Both have their own benefits and drawbacks. First, let's assume they are equally well designed. A two-way design tend to make it easier to integrate the two elements into a single sonic "picture" especially at shorter listening distances. A 3-way design tend to reduce distortion as each element is required to cover a smaller frequency span, but also making it more difficult to get them to "gel" into a single sonic "picture", Many times, a 3-way design will require more of a listening distance to get the 3 elements to blend.
Basically, select the one that fits your room and listening distance the best.