Yeah, the fact that this is based on the anime Vivid Strike, a sequel to the manga/anime Mahou Shoujou Lyrical Nanoha ViViD, a sequel to Mahou Shoujou Lyrical Nanoha StrikerS, a sequel to... kinda does land you in the deep end, characterization-wise.
The glasses-girl, Jill, is original to Vivid Strike; the other, Nove, goes back to StrikerS. Nove actually sums up her situation pretty well; she's both a cyborg and a clone, and if you think of the JS Incident she refers to as a large-scale terrorist attack, you won't be too far off. The protagonists thwarted the worst of it, she was arrested and rehabilitated, adopted by the widower of her genetic original, and as of Vivid Strike runs a gym for vaguely pubescent magical prize-fighters. Simple!