I am sorry. I'm not entirely sure why Nacchan can't return to tokyo. I got the idea she was bullied at school, but that seems like a childish thing to risk losing the love of her life over.
Painful experiences can really effect you for a long time and it seems that Tokyo just triggers bad memories for her. Besides the bullying it looks like her mother also left them to go back to Tokyo and now her lover is also leaving for Tokyo. So she probably associates Tokyo with a lot of negativity and it's a hard thing to break.
I don't think it will help their relationship much if she's constantly unhappy being in Tokyo even being with the love of her life. It might even destroy what they have.
I don't think this story had a bad ending. I just would have rather seen Nacchan overcome her fear of Tokyo, and gone with Kiri, in the end. separations in romance make me sad. Even if the couple get back together. I think of all the time they wasted apart.
It would've made for some nice character development yes, but with the limited time of a one shot it would've just come off as cheap, overly fast paced, irrealistic and underwhelming. If it was a series I would most definitely agree, but in a one shot I feel a time skip where there's no major developments but it just ties a nice end to it like this is more fitting.
I loved everything about this. The art, the realism feel, the story, the characters, the storytelling. Definitely up top in my favorite one shots.