Since this theme is going to be released soon. The greatest challenge about this theme was actually following the WordPress standards and allow fix all the Theme Testing rules that allow a theme to be easy for any WordPress install to be able to use it. Another of the greatest challenge that I faced was having to think ahead and pretty much guess what user controls anyone would want to have.
In order to comply with the Theme Unit Testing I had to read all the documentation plus see what TwentyEleven was doing in order to comply as well as actually fixing the error codes that the debugging tools prints all over the theme. In order to now what people want to have control I looked at themes that had a lot of sells in http://themeforest.net