The Setting is several years in the future of Earth. TSAB makes contact with Earth. They start a friendly trade agreement, but over time, jealousy about magic starts to get to the people of Earth and war breaks out.
I.e. Earth = Earth | TSAB = Zaft
Colonies were obviously set up as trade posts between TSAB and Earth, but a few remain neutral during the war.
Anyway, due to differences in military might vs magic, Earth is forced to research a way to emulate the magic type staffs with Technology. This leads to the creation of the staves.
Staves would be Raising Heart, Bardiche, and a few more I have yet to figure out the name of.
Nanoha, is obviously from Earth that had gone to the neutral colony to work as a civilian. She isn't aware of her Magical Potential.
Fate, has been a part of TSAB for quite a bit and was childhood friends with Nanoha. She is a part of the strike team that steals Bardiche.
Insert TSAB covert attack on the colony and Nanoha meets Fate while saving a yet named woman (who takes place of Murrue Ramius) and takes Raising Heart while Fate takes off with Bardiche.
Nanoha Battles Fate and co. to the Pacific, Orb, and beyond to...
Insert Berserk Nanoha and Fate Battle where Nanoha is defeated, seriously injuring Fate along the way.
Story continues to Alaska.
Insert Operation Spitbreak with Nanoha coming in with an upgraded Raising Heart(Belkan perhaps?) and Pwning ZAFT with her Accel Shooter.
Plot would basically remain the same, the story would have to be altered a little to incorporate Nanoha's ideals and responses.
Essentially,
Nanoha = Kira Yamato
Fate = Athrun Zala
Arisa and Suzuka = Earth friends (Sorry too lazy to look up)
Hayate and her Wolkenritter = Earth's prototype mages. (They don't have to die in the end)(Doesn't mean they can't be Befriended)
Not sure where to place Yuuno and Chrono other than the sides they are on. Maybe replace Lacus and Cagalli?
I was thinking Asura taking place of Archangel, but the Asura is a part of TSAB.
Mages would obviously be the new Coordinators, but they aren't made. They are born, which the people of Earth either don't believe or don't know.