I'm a girl with size 11 feet (kinda wide too..arg!), size 27 in Japan.
Preparing shoes to bring with me to Japan was also a big concern for me!! ^^
I pretty much gave up finding women's shoes here.... but there are other solutions

Although I brought my winter boots with me, if you are really hoping to save space in your suitcase for other things and don't mind spending the money later when the snow starts falling, you can probably just buy those once you've arrived in Japan.
Same goes for rain boots, unless you are attached to a pair you already own! Although I can't buy women's boots here, some of the men's ones look pretty "sleek" and feminine, so I just went with a basic black pair of those.
Also, indoor runners are something that may be optional for some of you depending on placements. I only brought my one pair of running shoes with me. Only now, almost 9 months into my stay here, have I finally bought indoor runners! Someone mentioned earlier in this thread that men's runners come in all sorts of colours (including pink!), which is very true! I just looked this week and they had a wide variety of many brand names like Nike, New Balance, etc, in various bright colour combinations. So even for girls with big feet, it would save you suitcase space to buy those kind of things later. (I can't buy women's running shoes in Canada anyway, so it wasn't really a big deal for me to wait until I got to Japan!) However, when I went back home at Christmas, I will admit I brought quite a few of my neglected pairs of heels that were waiting for me at home in Canada back to Japan with me...!!)
Main shoes I brought:
- 1 pair basic heels (orientation, first days to school, important events, etc)
- 1 pair sneakers (everyday)
- 1 pair of outdoor flats (heading to work)
- 1 pair of indoor flats (for schools)
- 1 pair of running shoes (for outdoors - if they are moderately clean, you could scrub the bottoms and they would be fine for indoor use too probably!!)
Could be bought in Japan, but brought with me anyways!:
- my winter boots - since they were snazzy I had them already! (I'm also living in Yamagata prefecture in the north. We get a LOT of snow)