While I agree that Sayaka just doesn't listen and Madoka is a bit weak in the knees at times, I don't get the other two at all.

I think it's just hairstyles. Although

just like Hanako is. If it was supposed to be based on some personality traits, then I think Lilly would fit in Mami's costume more than Misha.

But also: fans tend to put MSMM girls together in pairs: Madoka with Homura and Sayaka with Kyouko, leading to "lonely" Mami. And Misha is sort of "lonely" one in this game, considering that she doesn't have her own route.

Putting Misha as Madoka makes more sense, since her dynamic with Shizune is similar to Madoka and Sayaka's minus the yuri longing...or does it?

Except that in Madoka/Sayaka's case, Sayaka is acting like an idiot and Madoka (as well as the other girls) are trying to put some sense in her. Whereas in case of Misha/Shizune, Misha is sometimes acting like a fool and Shizune has to be her "voice" of reason (even if Misha is Shizune's voice).
If this one would be about personalities, then there's only one I can think of, who would fit in. And that's Lilly as Mami (as I said before).