Fantastic work honestly. I was really engaged throughout, and came to actually think about the characters as interesting and involved. The diary in particular I think did a lot to bring them all to life. Though the dialogue and overall concept is perhaps a bit more like, "Image Comics takes on magical girls", I think the end result overall worked out well, especially with Sakura playing the naive one and Gina as the more down-to-earth what-the-fuck-is-going-on person (with some experience). I'm not in love with the perhaps gratuitous usage of various insults, etc, which sort of made me think the story was going to be edgier than it turned out, but I think Sakura does a lot to take the sting out of it with her unending optimism. The ending was... a little pat (I honestly thought there would be a dialogue battle or something) but the scripted sequences and the way the story was overall set-up was fantastic.
To be honest, I'm not entirely sure why this was set up as a shooter; I think the style of game would have worked better almost as an adventure game or walking sim without the guns in some ways (combat aside). The interesting part was the interplay between the girls for the most part; I was perhaps the most bored when I was fighting characters, not least because they don't really flinch or have hit reactions and there's no real tactical element to that part of the game. I wasn't entirely sure what triggered the game to move on after 'firing on the archer in the forest', and I didn't figure out what the magic key was (or what the melee key was) until the farm. That said, the FPS controls and the gunplay worked relatively okay for the most part - this is coming off playing Deathloop for nearly a week straight - so I didn't have any particular issues with it either.
I have to be honest though, I really think you would benefit from teaming up with an artist. I came to enjoy the sprite rendering style in-game (it brings back memories of Duke Nukem 3D actually) but honestly, the portraits, background art, UI and suchlike was very distracting in... well, how amatuerish it looked. I was quite impressed with how much the drawings worked functionally, if that makes any sense, as backdrop or to convey certain impressions etc; but they absolutely did not work aesthetically and I think they sort of hold back the game from being as appealing as it could be. Obviously I don't know your workflow or the Unity workflow in general, but my guess is that a lot of stuff implementation wise would be pretty much 'drop this PNG in here' and a dedicated artist would do a lot to lighten that load.