WooCommerce Extension: Customize Emails
It's currently WAY too difficult to customize WooCommerce system emails. You should produce an extension that allows people more design flexibility and to customize the text easily. This is more than just a convenience- it's a branding and customer relations necessity.
I used a plugin called WP eStore before WooCommerce and they made it very easy to customize the various email text, complete with shortcodes you could use for order specific information (http://www.tipsandtricks-hq.com/ecommerce/wp-estore-shortcodes-and-functions-reference-460). Something like this would be very popular and make life a lot easier for people who need that kind of control.
This was completed earlier this year. Checkout WooCommerce Email Customizer: http://www.woothemes.com/products/woocommerce-email-customizer/
In WooCommerce 2.0 it will be standard. It has new options for individual transaction emails with template editor, so it is easier to change the text of your emails. 2.0 will come out in beginning of the new year.