Hmm it's well written for the most part.
But it barely feels like a Pokegirl story, I think if you had cut a lot of the everyone is magical and the Harry Potter Books, in reality it mostly feels like Harry crossing over into a mix of the real world and the pokegirl world and Harry Potter again.
Too much magic, I know magic also exist in the Pokegirl world but it's mostly Poke girls who have it, and the ones that do are actually more rare. The idea of a Magical Affairs Bureau in the seemingly half broken semi post apocalypse world of Pokegirls with things like marauders (not the Glue your shoes to the ground type, the Rape and Pillage type), rapist, and even town killing juggernauts running around with ease. A Magical Bureau feels like something a unified muggle/magical world would have right now, feels to clean and perfect. Add in the confusion with Nanoha's age, is she a Dimensional Cop chasing a criminal or is she younger than Harry, (I'm guessing your Harry is between 17 and 15, to age him up). I reality Nanoha feels like 2 characters slammed together, one a dimensional jumping love interest who had saved Harry and a Domestic Born Poke girl who had a teacher for a father and a stable quiet home life until she was ready to find a Tamer.
Remove the "crossovers" other than Harry and have the characters be OC's, the more characters you add that have to be important the more you have to balance the character you want in the pokegirl world and the character you are basing them on or are having cross right over. You have to decide if your writing a Harry/Pokegirls story or a massive Xover/Pokegirls story that is all about fan service.