Your flowers should keep with the fall color-scheme. You could have a wonderfully rich bouquet of not just red, orange or rust-colored roses, but you could also include deep colors of Gerber Daisies, Dahlias, Mums, Apricot Lilies, Rust/Burgundy hydrangea and Chrysanthemums. You can also include fall leaves, berries, or even miniature pinecones!
Flower girls can wear wreaths of these flowers and leaves in their hair. Instead of your flower girl dropping petals, they could drop leaves.