The Battlestar Luna, named for its first commander. Is, or uhh....was an experimental vessel. It was out on it's maiden voyage, quite far from the usual space used by colonial ships. The Battlestar Luna, the only fully-pony operated ship was meant to be a research and exploration. These reason behind this was: the general population didn't like the ponies all that much. Too many brightly colored animals and such. The only reason any ponies had risen to any part of the colonial military was because many of them were as smart as any human. Most were also quick-thinkers, and very resourceful, making them hard to kill or disable. When the Cylons attacked the colonies they had not anticipated a threat from small colorful ponies and their winged leadership...

but not from Equestria. These are versions of them formed in a separate galaxy by astronomical improbability. Formed on colonies...