Well the Xindi thought of the sphere builders as Gods. Degra admitted that he was raised since boyhood to revere them and their words as truth. Reptillians and Insectoids were just itching for a conflict harder than the other 3 races. Not like we haven't seen other races in Trek that were overly devoted to those they perceived as gods. Bajorans and the Prophets anyone?
I like the arc and generally satisfied with how it went. Some episodes like Extinction, Exile, Twilight, North Star, Similitude, Doctor's Orders (blatant repeat of VOY episode One), Hatchery and E2 could've been cut and really are filler episodes and or filler mixed with plot.