An issue for the Omega theme requested color module support. The issue received a closed, won't fix status on the rationale that color support needs to be built into the sub-theme. The color module is reported to not provide very good support for themes like Omega that are meant to be implemented using sub themes.
Since the Subtheme Wizard of Omega Tools creates a sub theme from Omega, it seems like a logical place to add support for the color module. So, I hereby make such a request.