I'm kind of confused whether Haruki is meant to be trans or trans-coded or not. It doesn't really feel that way from the game, but the key art is almost literally the colours of the trans flag.
It's really unclear initially which character is which, because both characters are shown on screen at the same time and the text doesn't make it clear who is who. I didn't figure out which one was Haru and which one was Chi-Chi until the hug scene.
I didn't fully understand what was going on the first time, but the second time I played it all clicked. For me the twist and the big reveal almost, but didn't quite work. I can't put my finger on why that is. Maybe it's because the connection between the magical girl battle and the later event wasn't clear, maybe it's because there doesn't really seem to be a motive past "yandere gonna yandere". This is probably something that can be addressed pretty well with a little tweaking.
I thought the art wouldn't really be my thing, but it's surprisingly appealing. I do wish there was sound and music. You mentioned that this isn't complete, though, so I'm assuming those are on the to-do list.
The battle system is, uh, sorry, it's just not very good. I realize doing that in RenPy is hard and it's not really the focus of the game, but it's hard to give a pass to when I've seen much better ones in the past. A Magical Girl's Duty (sadly never finished) from the first MGGJ was particularly good. Even if you choose to keep it simple, I'd like to see the presentation improved.
I think it's a good start. The storyline can work, the art style is good. A few things are missing and a few things could be tweaked. But I'm looking forward to playing the finished game.