How about an option to have an alternating two color board for the nine largest squares? Many sudokus use this type of format. Your program alows for nine different colors or one color. I think that a two color format would be more useful than a nine color format.
I believe this is a good request. My newspaper prints sudoku puzzles using this format and it helps to separate the large squares in my mind. So count at least one other person who would like to see this option.