Good question. 
Again, I think the aforementioned Agama Research Group are doing wonderful things with comparative studies.
Unsurprisingly, comparative studies are not popular with most mainstream establishments, since they bring text-critical/text-historical approaches to the study of the Buddhist teachings, and very few traditions want to be challenged for the provenance of their scriptures.
This can have varying effects on the confidence a practitioner has on the scriptures and the traditions they are built on. The downsides of challenging the establishments are obvious — what may not be immediately obvious is why a critical perspective might in fact increase confidence.
Of course, some might prefer to consider the entire canon to be verbatim faithful to the dot to every details of Buddha’s and his disciples’ lives. While I can respect that as a practice position (many respectable monastics and practitioners can be considered here), some may also find it hard to defend as a correct historical assessment of the transmission, which is likewise the view of too many monastics.
Some of the more fantastical, harder to process stories can be read as an insightful product of a monastic community who skillfully shaped their stories to meet the needs of the audiences. Some stories, read allegorically, or as literary answers to certain Brahmanical stories and tropes, can prove to be quite insightful.
Furthermore, Agamas being the backbone of all Buddhist traditions, a communal EBTS like the ARG, can provide scholarship to the links between different schools.
An immediate example would be Prajnaparamita Sutras in Mahayana. Both Theravadins and Mahayanists might think it differs significantly from EBTs, but upon close research, like Ven. Analayo’s Work, we might trace how its ideas are found across Agamas.
All in all, a careful study of comparative Buddhist EBTs can help us understand how the canon was shaped and so understand our own history better, and bring otherwise estranged communities together. I think these are good things, overall.