It's so rare to find a mecha manga with a female protagonist and mostly female cast that isn't made for the sake of fanservice, which makes it all the more disappointing that this one turned out so poorly.
STELLVIA (Uchu no Suturuvia), based on the anime series by Xebec with art by Ryo Akitsuki. First published in 2003 and first published in North America in 2005.
PLOT:
Nearly 200 years ago, Earth was ravaged by a massive electromagnetic wave from a supernova. Even decades later, the night skies are still tinged with green. That's the reason that Shima Katose wants to become a space pilot: to see what the stars truly look like. She manages to get into the illustrious space academy Stellvia and makes some friends, but she struggles with her piloting courses. What she and her friends don't know is that the second wave of radiation is only a few months away...