We appreciate the feedback. Theme it is definitely designed for the new user that isn't as comfortable with hand coding.
The concept is to take a color-centric and image-centric approach to making changes since we find many new users say they just want to change a color or an image and can't figure out where in the page or .css to find and make that change.
Even though it may not work on all pages at first, we will be able to update our solutions and product output to work very well with theme it for customization. There will be plenty of room to add features and improve this v1 product.
We definitely appreciate the suggestions and first impressions and will try to work out some of the issues you have described.