This is a list of questions I have found to help me in dealing with all of this chaos.

The first question is existential. The more you work with species complexes, the more you come to see this category we call species as a human cognative convenience. This question helps you keep things in perspective.

The second question is partially answered by our systems analysis model of the gerrmplasm, environment and history system. Species that dont have fuzzy boundaries cant, shouldnt, or it just didnt.

The next two questions are specific questions to be asked about taxa that can help assess the importance of each factor contributing to the fuzzy species system. If someone (like your major professor) discounts the significance of a group of taxa with unclear boundaries, by saying it is obviously just in the early stages of divergence, you might ask these questions just to shake the tree and wake them up.