Character themes would be cool to hear eventually, but I like that they went with stage themes to start with. World-building is much more important for Skullgirls than MvC, so it's good that while we're interacting with the characters, the themes help to establish the tone of the environments they live in. If character themes are ever added later, that'll just mean a more robust soundtrack overall.
To your question though, I'd speculate that early in development, it was just easier for them to figure out the number of stages they could develop by the release date. They wouldn't want to pay for 9 character themes if only 7 characters were going to make it out the door, or somehow squeeze out 10 characters and have to commission an extra theme on short notice. So, once Yamane was signed up, they probably just felt stage themes would be a more economical use of her time and talents.