Five Star Monogatari

From Anime News Network:
Several thousands of years from now, there exists the Joker Galaxy of five Star Systems, where a long, long war is being fought. The god of light, Amaterasu, is trying to unite the galaxy under his rule. The fighting stands between giant mecha called Mortar Headds, their pilots, the Headdliners, trained since birth for their task, and the female humanlike computers called Fatimas, necessary for controlling the MH. Many are the lives and destinies found throughout the more than thousand year long era of war, although Amaterasu seems to live through it all.
Note: To honor its 25th anniversary, the series was reprinted under Five Star Monogatari Reboot (The Five Star Stories Reboot) with a final and 13th volume.