The primary disadvantage of excision is that it is fairly non-selective. If the endometriosis being removed is far away from vital structures, then excision is a good approach. If the endometriosis is growing on vital structures, I feel excision is a poor choice, as it may result in the removal of normal vital structures. In my opinion, if endometriosis is aggressively removed using only excision, there will be a higher incidence of bowel resection, ureteral resection etc. First, coagulation is usually performed using an electrical current that is passed through the body.
Coagulation is in essence an electrical burn that destroys the appearance of the tissue.
As a result, it is impossible to tell what is normal and what is abnormal. Since the surgeon can't tell if all of the endometriosis has been destroyed, deep endometriosis can and is left behind. In the worst case normal peritoneum heals over this area with endometriosis deep underneath. The longer the tissue is coagulated, the deeper the damage but the degree of damage is not apparent for days or even a week. If the surgeon were to over treat, the thermal damage from the coagulation would damage the normal underlying vital structure, i.e. the bowel in this example.