In regard to the cylons, I feel what ruined the show there was that they had no clear motivation.
They bombed the colonies and dropped hints that there was an ulterior motive for this ("And they have a plan...") but it seems to me the writers never did. They kept the mystery and drama of what the Cylons wanted up in the air but offered contradicting clues as to what that plan was. They wanted to harvest ovaries. They wanted to outgrow their parents. Etx. In the end, didn't Eick admit that they slapped on "And they have a plan" because it sounded cool, and for no other reason?
Other villains, even ones that reform, have some reason for doing what they did to the protagonists. The Borg want to make everyone perfect, so they assimilate people. The Galactic Empire from Star wars wanted to oppress everybody, so they built a giant death station. Shaddam the IVth feared the influence of house Atreadies , so he backstabbed them politically. The original cylons hated humanity's unpredictability, so they must be killed.
Moore's cylons? God did it. Apparently God made the cylons blow up the colonies so the radioactive, socially backward remnants could bounce across the universe, breed with the cylons, and give hera to Earth. That premise alone sounds as convoluted as some bad fanfiction, yet that seems to be what we're left with, no? And yet Moore gets gushing praise for "The best Sci-fi show on television".