Releasing plot bunny into the wild!
Crossing over Infinite Stratos with Blazblue.
Replace the IS with the Murakumo units. Only women can use the murakumo units because all murakumo units follow the original amaterasu unit design which was gene locked to a woman. So even amongst women, only certain women can use a murakumo due to DNA lock.
Ichika is an exception, because technically, he doesn't get a murakumo. Instead he gets a complete blazblue. A complete "cauldron" or mechanism that creates these murakumos.
Years ago, his house is ransacked right before the announcement of the IS that Chifuyu was test piloting for her best friend and IS inventor, Shinonono Tabane. Chifuyu is kidnapped and so the IS is test piloted by another pilot. During the testing, a unit descends upon the test site. Despite the PIC and beam weaponry found on the first generation IS unit White Knight, it found itself outmatched. It left the world agape as the exo-armor known to be decades if not centuries ahead of whatever the world had today was easily crushed. This unknown unit seemed to exhibit every single capability of the IS, only far more advanced with many of its capabilities activating merely on thoughts of the pilot. It also exhibited high mobility that resembled instantaneous translocation as well as dimensional manipulation. The machine proclaimed itself as Amaterasu and that the world would end soon. It hacks the IS reseach mainframe and begins to load a vast database onto it. Amaterasu tells them that "the world must gather its resources for time is short. The Beasts will awaken and ravage this world. Fed by the impurities it will continue to consume all.".
Ichika lives a normal life, relatively normal as he lives alone but regularly visited by the Gotanda Ran. He tries to be a bit more cheerful despite the tragedy that took his sister away from him, as well as his arm which was replaced by a black prosthetic, despite how natural it seemed to work. On the day of his highschool entrance exam, Ichika's arm reacts to a selection test for murakumo pilots. Ichkika is pulled in by the government and finds himself under the wing and protective custody of Tabane, the scientist assigned to dissect him. To honoer Chifuyu, she instead sends him to the murakumo
dojo, a giant school dedicated to the study of murakumo units and training of its pilots.
The IS aren't completely removed. Just relegated to the
slightly less special 
Armagus, weapons that cannot be explained by science but derived from the technology passed on by Amaterasu. These can be used by anyone, however much like any art or skill, use of armagus is relative to talent and hardwork.
EDIT: Just heard megaman X7's opening theme. For some reason I find it very fitting for IS had they decided to make it take the mecha side seriously. It helps a lot that the title of the song is Code Crush.