Ken En Ken: Aoki Kagayaki

Both were set in a certain time period where warring factions fight for supremacy, except one was set in some quasi european setting while the other is more on the oriental east, one was more of supernatural and fantasy while the other has an odd kind of sci-fi in it.  

Both have the same Action, Military and mecha genres, and a certain character who works for the enemy despite of all the shitty thing he has experience from them.  

Both have the same story plot of a group of people whom were out to fight an evil empire, where the one in the helm is a girl with such sword skills and special powers.